Publications of the group
access_time
January 26 2022
2022
2021
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Model Folded Hydrophobic Polymers Reside in Highly Branched Voids
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, (2021)
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Statistically unbiased free energy estimates from biased simulations
MOLECULAR PHYSICS, 119 (19-20) (2021)
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Investigating the Molecular Mechanism of H3B-8800: A Splicing Modulator Inducing Preferential Lethality in Spliceosome-Mutant Cancers
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 22 (20) (2021)
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Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles
NUCLEIC ACIDS RESEARCH, 49 (14) (2021)
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Nanorheology of active-passive polymer mixtures differentiates between linear and ring polymer topology
SOFT MATTER, 17 (30) pp.7111-7117 (2021)
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Tunable Knot Segregation in Copolyelectrolyte Rings Carrying a Neutral Segment
ACS MACRO LETTERS, 10 (11) pp.1365-1370 (2021)
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Comparing state-of-the-art approaches to back-calculate SAXS spectra from atomistic molecular dynamics simulations
EUROPEAN PHYSICAL JOURNAL B, 94 (9) (2021)
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Polymer Physics by Quantum Computing
PHYSICAL REVIEW LETTERS, 127 (8) (2021)
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essHi-C: essential component analysis of Hi-C matrices
BIOINFORMATICS, 37 (15) pp.2088-2094 (2021)
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Unfolding and Translocation of Knotted Proteins by Clp Biological Nanomachines: Synergistic Contribution of Primary Sequence and Topology Revealed by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 125 (27) pp.7335-7350 (2021)
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Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 143 (22) pp.8333-8343 (2021)
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RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration
JOURNAL OF PHYSICAL CHEMISTRY B, 125 (4) pp.1098-1106 (2021)
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Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 12 (25) pp.5987-5993 (2021)
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Arginine multivalency stabilizes protein/RNA condensates
PROTEIN SCIENCE, 30 (7) pp.1418-1426 (2021)
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Molecular Mechanisms of the Blockage of Glioblastoma Motility
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 61 (6) pp.2967-2980 (2021)
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Deciphering the Molecular Terms of Arp2/3 Allosteric Regulation from All-Atom Simulations and Dynamical Network Theory
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 12 (22) pp.5384-5389 (2021)
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Frontiers of metal-coordinating drug design
EXPERT OPINION ON DRUG DISCOVERY, 16 (5) pp.497-511 (2021)
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All-atom simulations to studying metallodrugs/target interactions
CURRENT OPINION IN CHEMICAL BIOLOGY, 61 pp.1-8 (2021)
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Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation
BMC BIOINFORMATICS, 22 (1) (2021)
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A Rosetta-based protein design protocol converging to natural sequences
JOURNAL OF CHEMICAL PHYSICS, 154 (7) (2021)
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Atomic-Level Mechanism of Pre-mRNA Splicing in Health and Disease
ACCOUNTS OF CHEMICAL RESEARCH, 54 (1) pp.144-154 (2021)
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2020
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Machine learning a model for RNA structure prediction
NAR GENOMICS AND BIOINFORMATICS, 2 (4) (2020)
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Data segmentation based on the local intrinsic dimension
SCIENTIFIC REPORTS, 10 (1) (2020)
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Peptide Inhibitors of Bacterial Protein Synthesis with Broad Spectrum and SbmA-Independent Bactericidal Activity against Clinical Pathogens
JOURNAL OF MEDICINAL CHEMISTRY, 63 (17) pp.9590-9602 (2020)
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Toward empirical force fields that match experimental observables
JOURNAL OF CHEMICAL PHYSICS, 152 (23) (2020)
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Is the Rigidity of SARS-CoV-2 Spike Receptor-Binding Motif the Hallmark for Its Enhanced Infectivity? Insights from All-Atom Simulations
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 11 (12) pp.4785-4790 (2020)
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Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 16 (6) pp.3936-3946 (2020)
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Merging 1D and 3D genomic information: Challenges in modelling and validation
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS, 1863 (6) (2020)
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MicroMotility: State of the art, recent accomplishments and perspectives on the mathematical modeling of bio-motility at microscopic scales
MATHEMATICS IN ENGINEERING, 2 (2) pp.230-252 (2020)
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Metadynamics: A Unified Framework for Accelerating Rare Events and Sampling Thermodynamics and Kinetics
Handbook of Materials Modeling pp 565-595
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Pressure control using stochastic cell rescaling
JOURNAL OF CHEMICAL PHYSICS, 153 (11) (2020)
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Separation of Geometrical and Topological Entanglement in Confined Polymers Driven out of Equilibrium
ACS MACRO LETTERS, 9 (8) pp.1081-1085 (2020)
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Directional translocation resistance of Zika xrRNA
NATURE COMMUNICATIONS, 11 (1) (2020)
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Decrypting the Information Exchange Pathways across the Spliceosome Machinery
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 142 (18) pp.8403-8411 (2020)
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Assessing the accuracy of direct-coupling analysis for RNA contact prediction
RNA, 26 (5) pp.637-647 (2020)
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Using metadynamics to explore complex free-energy landscapes
NATURE REVIEWS PHYSICS, 2 (4) pp.200-212 (2020)
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All-Atom Simulations Disclose How Cytochrome Reductase Reshapes the Substrate Access/Egress Routes of Its Partner CYP450s
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 11 (4) pp.1189-1193 (2020)
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Conformational ensembles of an RNA hairpin using molecular dynamics and sparse NMR data
NUCLEIC ACIDS RESEARCH, 48 (3) pp.1164-1174 (2020)
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Explicit Characterization of the Free-Energy Landscape of a Protein in the Space of All Its C-alpha Carbons
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 16 (1) pp.80-87 (2020)
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2019
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Intrinsic dimension of data representations in deep neural networks
ADVANCES IN NEURAL INFORMATION PROCESSING SYSTEMS 32 (NIPS 2019), 32 (2019)
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Analyzing and Biasing Simulations with PLUMED
BIOMOLECULAR SIMULATIONS: METHODS AND PROTOCOLS, 2022 pp.529-578 (2019)
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A common root for coevolution and substitution rate variability in protein sequence evolution
SCIENTIFIC REPORTS, 9 (2019)
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Topological Constraints in Eukaryotic Genomes and How They Can Be Exploited to Improve Spatial Models of Chromosomes
FRONTIERS IN MOLECULAR BIOSCIENCES, 6 (2019)
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Asymmetric base-pair opening drives helicase unwinding dynamics
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 116 (45) pp.22471-22477 (2019)
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TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami
JOURNAL OF COMPUTATIONAL CHEMISTRY, 40 (29) pp.2586-2595 (2019)
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Promoting transparency and reproducibility in enhanced molecular simulations
NATURE METHODS, 16 (8) pp.670-673 (2019)
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Microrheology of interphase chromosomes with spatial constraints: a computational study
PHYSICAL BIOLOGY, 16 (6) (2019)
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Spontaneously Forming Dendritic Voids in Liquid Water Can Host Small Polymers
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 10 (18) pp.5585-5591 (2019)
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Promiscuous nature of liquid water: Profiling its density and charge fluctuations
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 258 (2019)
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Transcriptional supercoiling boosts topoisomerase II-mediated knotting of intracellular DNA
NUCLEIC ACIDS RESEARCH, 47 (13) pp.6946-6955 (2019)
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The pivotal role of MBD4-ATP7B in the human Cu(i) excretion path as revealed by EPR experiments and all-atom simulations
METALLOMICS, 11 (7) pp.1288-1297 (2019)
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Statistical mechanical properties of sequence space determine the efficiency of the various algorithms to predict interaction energies and native contacts from protein coevolution
PHYSICAL BIOLOGY, 16 (4) (2019)
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Hydrodynamics and Filtering of Knotted Ring Polymers in Nanochannels
MACROMOLECULES, 52 (11) pp.4111-4119 (2019)
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Fitting Corrections to an RNA Force Field Using Experimental Data
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 15 (6) pp.3425-3431 (2019)
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Tuning the hydrogen-bonding interactions of the AMBER RNA force field
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 37 pp.50-51 (2019)
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Unraveling the molecular mechanisms of color expression in anthocyanins
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 21 (17) pp.8757-8766 (2019)
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Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 15 (5) pp.3288-3305 (2019)
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The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models
JOURNAL OF CHEMICAL PHYSICS, 150 (15) (2019)
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The Subtle Trade-Off between Evolutionary and Energetic Constraints in Protein-Protein Interactions
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 10 (7) pp.1489-1497 (2019)
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Can multiscale simulations unravel the function of metallo-enzymes to improve knowledge-based drug discovery?
FUTURE MEDICINAL CHEMISTRY, 11 (7) pp.771-792 (2019)
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Topologically Linked Chains in Confinement
ACS MACRO LETTERS, 8 (4) pp.442-446 (2019)
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The intrinsic dimension of protein sequence evolution
PLOS COMPUTATIONAL BIOLOGY, 15 (4) (2019)
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Local loop opening in untangled ring polymer melts: a detailed "Feynman test" of models for the large scale structure
SOFT MATTER, 15 (11) pp.2418-2429 (2019)
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Dynamics of Supercoiled Knotted DNA: Large Scale Rearrangements and Persistent Multi Strand Interlocking
BIOPHYSICAL JOURNAL, 116 (3) (2019)
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Clustering and Identification of Force Spectra from Native Membranes
BIOPHYSICAL JOURNAL, 116 (3) (2019)
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Microrheology of Interphase Nuclei: A Computer Simulation Study
BIOPHYSICAL JOURNAL, 116 (3) (2019)
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Barnaba: software for analysis of nucleic acid structures and trajectories
RNA, 25 (2) pp.219-231 (2019)
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Threading of Unconcatenated Ring Polymers at High Concentrations: Double-Folded vs Time-Equilibrated Structures
ACS MACRO LETTERS, 8 (2) pp.155-160 (2019)
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Bimodality in the knotting probability of semiflexible rings suggested by mapping with self-avoiding polygons
REACTIVE & FUNCTIONAL POLYMERS, 134 pp.141-149 (2019)
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Conformational statistics of randomly branching double-folded ring polymers
EUROPEAN PHYSICAL JOURNAL E, 42 (1) (2019)
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2018
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Protein ORIGAMI: A program for the creation of 3D paper models of folded peptides
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 46 (4) pp. 403-409 (2018)
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Discovering privileged topologies of molecular knots with self-assembling models
NATURE COMMUNICATIONS, 9 (2018)
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The Ising model in swollen vs. compact polymers: Mean-field approach and computer simulations
EUROPEAN PHYSICAL JOURNAL E, 41 (12) (2018)
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Determination of Structural Ensembles of Proteins: Restraining vs Reweighting
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 14 (12) pp.6632-6641 (2018)
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Preface: Special Topic on Enhanced Sampling for Molecular Systems
JOURNAL OF CHEMICAL PHYSICS, 149 (7) (2018)
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A Dehydrogenase Dual Hydrogen Abstraction Mechanism Promotes Estrogen Biosynthesis: Can We Expand the Functional Annotation of the Aromatase Enzyme?
CHEMISTRY-A EUROPEAN JOURNAL, 24 (42) pp. 10840-10849 (2018)
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Toward a unified scoring function for native state discrimination and drug-binding pocket recognition
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 20 (25) pp. 17148-17155 (2018)
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Electric-Field-Driven Trapping of Polyelectrolytes in Needle-like Backfolded States
MACROMOLECULES, 51 (12) pp. 4462-4470 (2018)
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All-atom simulations disentangle the functional dynamics underlying gene maturation in the intron lariat spliceosome
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 115 (26) pp. 6584-6589 (2018)
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KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers
EUROPEAN PHYSICAL JOURNAL E, 41 (6) (2018)
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Foreword
JOURNAL OF BIOLOGICAL PHYSICS, 44 (2) pp.117-117 (2018)
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Vibrational entropy estimation can improve binding affinity prediction for non-obligatory protein complexes
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 86 (4) pp.393-404 (2018)
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Nanoprobe diffusion in entangled polymer solutions: Linear vs. unconcatenated ring chains
JOURNAL OF CHEMICAL PHYSICS, 148 (19) (2018)
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Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations
SCIENCE ADVANCES, 4 (5) (2018)
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Exploring RNA structure and dynamics through enhanced sampling simulations
CURRENT OPINION IN STRUCTURAL BIOLOGY, 49 pp.63-71 (2018)
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Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered molecular dynamics
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 498 (2) pp.352-358 (2018)
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Computing the Free Energy without Collective Variables
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 14 (3) pp.1206-1215 (2018)
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A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs
NUCLEIC ACIDS RESEARCH, 46 (4) pp.1674-1683 (2018)
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Compactness of viral genomes: effect of disperse and localized random mutations
JOURNAL OF PHYSICS-CONDENSED MATTER, 30 (8) (2018)
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Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1
SCIENTIFIC REPORTS, 8 (2018)
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Peptide biosensors for anticancer drugs: Design in silico to work in denaturizing environment
BIOSENSORS & BIOELECTRONICS, 100 pp.298-303 (2018)
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Binding affinity prediction of nanobody-protein complexes by scoring of molecular dynamics trajectories
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 20 (5) pp.3438-3444 (2018)
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The Interplay between Structural Stability and Plasticity Determines Mutation Profiles and Chaperone Dependence in Protein Kinases
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 14 (2) pp.1059-1070 (2018)
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Automated Force-Field Parametrization Guided by Multisystem Ensemble Averages
BIOPHYSICAL JOURNAL, 114 (3) (2018)
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Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 9 (2) pp.313-318 (2018)
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A Computational Assay of Estrogen Receptor alpha Antagonists Reveals the Key Common Structural Traits of Drugs Effectively Fighting Refractory Breast Cancers
SCIENTIFIC REPORTS, 8 (2018)
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The interaction of Schiff Base complexes of nickel(II) and zinc(II) with duplex and G-quadruplex DNA
JOURNAL OF INORGANIC BIOCHEMISTRY, 178 pp.106-114 (2018)
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Exact and Efficient Sampling of Conditioned Walks
JOURNAL OF STATISTICAL PHYSICS, 170 (1) pp.79-100 (2018)
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2017
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Phase Coexistence in Two-Dimensional Passive and Active Dumbbell Systems
PHYSICAL REVIEW LETTERS, 119 (26) (2017)
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Patterns of coevolving amino acids unveil structural and dynamical domains
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114 (50) (2017)
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Mapping the Chemical Space of the RNA Cleavage and Its Implications for Ribozyme Catalysis
JOURNAL OF PHYSICAL CHEMISTRY B, 121 (48) pp.10828-10840 (2017)
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Direct in silico visualization of ligands channelling through proteins: The next-generation frontier of computational biology Comment on Tigand diffusion via enhanced sampling molecular dynamics' by Jakub Rydzewski and Wieslaw Nowak
PHYSICS OF LIFE REVIEWS, 22-23 pp.82-84 (2017)
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Effect of Nematic Ordering on the Elasticity and Yielding in Disordered Polymeric Solids
JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, 55 (23) pp.1760-1769 (2017)
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Glassiness and Heterogeneous Dynamics in Dense Solutions of Ring Polymers
PHYSICAL REVIEW LETTERS, 119 (19) (2017)
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Polymer models with optimal good-solvent behavior
JOURNAL OF PHYSICS-CONDENSED MATTER, 29 (43) (2017)
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A Markov state modeling analysis of sliding dynamics of a 2D model
JOURNAL OF CHEMICAL PHYSICS, 147 (15) (2017)
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Large Fluctuations and Dynamic Phase Transition in a System of Self-Propelled Particles
PHYSICAL REVIEW LETTERS, 119 (15) (2017)
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Predicting Amino Acid Substitution Probabilities Using Single Nucleotide Polymorphisms
GENETICS, 207 (2) pp.643-652 (2017)
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Estimating the intrinsic dimension of datasets by a minimal neighborhood information
SCIENTIFIC REPORTS, 7 (2017)
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New views on phototransduction from atomic force microscopy and single molecule force spectroscopy on native rods
SCIENTIFIC REPORTS, 7 (2017)
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Mechanical Pulling of Linked Ring Polymers: Elastic Response and Link Localisation
POLYMERS, 9 (8) (2017)
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An omics perspective to the molecular mechanisms of anticancer metallo-drugs in the computational microscope era
EXPERT OPINION ON DRUG DISCOVERY, 12 (8) pp.813-825 (2017)
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METAGUI 3: A graphical user interface for choosing the collective variables in molecular dynamics simulations
COMPUTER PHYSICS COMMUNICATIONS, 217 pp.204-209 (2017)
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Two-qubit correlations revisited: average mutual information, relevant (and useful) observables and an application to remote state preparation
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL, 50 (29) (2017)
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Non-monotonic knotting probability and knot length of semiflexible rings: the competing roles of entropy and bending energy
SOFT MATTER, 13 (23) pp.4260-4267 (2017)
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Efficient Sampling of Knotting-Unknotting Pathways for Semiflexible Gaussian Chains
POLYMERS, 9 (6) (2017)
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Spatial confinement induces hairpins in nicked circular DNA
NUCLEIC ACIDS RESEARCH, 45 (8) pp.4905-4914 (2017)
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Single or Multiple Access Channels to the CYP450s Active Site? An Answer from Free Energy Simulations of the Human Aromatase Enzyme
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 8 (9) pp.2036-2042 (2017)
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Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1861 (5) pp.1246-1263 (2017)
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Unraveling Mg2+-RNA binding with atomistic molecular dynamics
RNA, 23 (5) pp.628-638 (2017)
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Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides
RNA, 23 (5) pp.712-720 (2017)
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Influence of Linker Flexibility on the Binding Affinity of Bidentate Binders
JOURNAL OF PHYSICAL CHEMISTRY B, 121 (16) pp.3918-3924 (2017)
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Physical Links: defining and detecting inter-chain entanglement
SCIENTIFIC REPORTS, 7 (2017)
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Pore translocation of knotted DNA rings
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114 (15) (2017)
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Thermal compaction of the intrinsically disordered protein tau: entropic, structural, and hydrophobic factors
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 19 (12) pp.8435-8446 (2017)
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fMRI Single Trial Discovery of Spatio-Temporal Brain Activity Patterns
HUMAN BRAIN MAPPING, 38 (3) pp.1421-1437 (2017)
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Self-assembly of knots and links
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, (2017)
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Linking of Ring Polymers in Slit-Like Confinement
MACROMOLECULES, 50 (4) pp.1713-1718 (2017)
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Feasibility and coexistence of large ecological communities
NATURE COMMUNICATIONS, 8 (2017)
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Fibrillation-prone conformations of the amyloid-beta-42 peptide at the gold/water interface
NANOSCALE, 9 (6) pp.2279-2290 (2017)
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Flory theory of randomly branched polymers
SOFT MATTER, 13 (6) pp.1223-1234 (2017)
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How to fold intricately: using theory and experiments to unravel the properties of knotted proteins
CURRENT OPINION IN STRUCTURAL BIOLOGY, 42 pp.6-14 (2017)
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Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 13 (2) pp.926-934 (2017)
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From conformational spread to allosteric and cooperative models of E. coli flagellar motor
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, (2017)
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Unifying view of mechanical and functional hotspots across class A GPCRs
PLOS COMPUTATIONAL BIOLOGY, 13 (2) (2017)
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Sorting ring polymers by knot type with modulated nanochannels
SOFT MATTER, 13 (4) pp.795-802 (2017)
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Computational design of cyclic peptides for the customized oriented immobilization of globular proteins
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 19 (4) pp.2740-2748 (2017)
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Beyond Flory theory: Distribution functions for interacting lattice trees
PHYSICAL REVIEW E, 95 (1) (2017)
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Single-Molecule FRET Measurements in Additive-Enriched Aqueous Solutions
ANALYTICAL CHEMISTRY, 89 (1) pp.694-702 (2017)
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Development of Site-Specific Mg2+-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 13 (1) pp.340-352 (2017)
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2016
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Tuning knot abundance in semiflexible chains with crowders of different sizes: a Monte Carlo study of DNA chains
SOFT MATTER , 12 (32) pp. 6708-6715 (2016)
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Enzymatic and Inhibition Mechanism of Human Aromatase (CYP19A1) Enzyme. A Computational Perspective from QM/MM and Classical Molecular Dynamics Simulations
MINI-REVIEWS IN MEDICINAL CHEMISTRY , 16 (14) pp. 1112-1124 (2016)
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The molecular mechanism of secondary sodium symporters elucidated through the lens of the computational microscope
RSC ADVANCES , 6 (12) pp. 9522-9540 (2016)
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Modeling quorum sensing trade-offs between bacterial cell density and system extension from open boundaries
SCIENTIFIC REPORTS , 6 (2016)
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Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement
JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 12 (12) pp. 6192-6200 (2016)
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Improved model for mixtures of polymers and hard spheres
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL , 49 (50) (2016)
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Markov state modeling of sliding friction
PHYSICAL REVIEW E , 94 (5) (2016)
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Computer simulations of melts of randomly branching polymers
JOURNAL OF CHEMICAL PHYSICS , 145 (16) (2016)
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Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization
SCIENTIFIC REPORTS , 6 (2016)
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Free Energy Landscape of GAGA and UUCG RNA Tetraloops
JOURNAL OF PHYSICAL CHEMISTRY LETTERS , 7 (20) pp. 4032-4038 (2016)
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Structural, dynamical and catalytic interplay between Mg2+ ions and RNA. Vices and virtues of atomistic simulations
INORGANICA CHIMICA ACTA , 452 pp. 73-81 (2016)
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Sampling Molecular Conformers in Solution with Quantum Mechanical Accuracy at a Nearly Molecular-Mechanics Cost
JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 12 (9) pp. 4385-4389 (2016)
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Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies
JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 12 (9) pp. 4534-4548 (2016)
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Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , 84 (9) pp. 1312-1320 (2016)
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Computer simulations of randomly branching polymers: annealed versus quenched branching structures
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL , 49 (34) (2016)
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Who Activates the Nucleophile in Ribozyme Catalysis? An Answer from the Splicing Mechanism of Group II Introns
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY , 138 (33) pp. 10374-10377 (2016)
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Permeability Coefficients of Lipophilic Compounds Estimated by Computer Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 12 (8) pp. 4093-4099 (2016)
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Optimal Self-Assembly of Linked Constructs and Catenanes via Spatial Confinement
ACS MACRO LETTERS , 5 (8) pp. 931-935 (2016)
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Phase Diagram and Structure of Mixtures of Large Colloids and Linear Polymers under Good-Solvent Conditions
MACROMOLECULES , 49 (14) pp. 5266-5280 (2016)
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Metadynamics surfing on topology barriers: the CPN-1 case
JOURNAL OF HIGH ENERGY PHYSICS , (7) (2016)
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RNA folding pathways in stop motion
NUCLEIC ACIDS RESEARCH , 44 (12) pp. 5883-5891 (2016)
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Non-Markovian effects on protein sequence evolution due to site dependent substitution rates
BMC BIOINFORMATICS , 17 (2016)
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Fighting Cancer with Transition Metal Complexes: From Naked DNA to Protein and Chromatin Targeting Strategies
CHEMMEDCHEM , 11 (12) pp. 1199-1210 (2016)
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Fusing simulation and experiment: The effect of mutations on the structure and activity of the influenza fusion peptide
SCIENTIFIC REPORTS , 6 (2016)
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Large Scale Chromosome Folding Is Stable against Local Changes in Chromatin Structure
PLOS COMPUTATIONAL BIOLOGY , 12 (6) (2016)
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Empirical Corrections to the Amber RNA Force Field with Target Metadynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 12 (6) pp. 2790-2798 (2016)
doi: -
Paired arrangement of kinetochores together with microtubule pivoting and dynamics drive kinetochore capture in meiosis I
SCIENTIFIC REPORTS , 6 (2016)
doi: -
A molecule that detects the length of DNA by using chain fluctuations
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT , (2016)
doi: -
Tracer motion in an active dumbbell fluid
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT , (2016)
doi: -
Global coherence of quantum evolutions based on decoherent histories: Theory and application to photosynthetic quantum energy transport
PHYSICAL REVIEW A , 93 (4) (2016)
doi: -
Role of Enzyme Flexibility in Ligand Access and Egress to Active Site: Bias-Exchange Metadynamics Study of 1,3,7-Trimethyluric Acid in Cytochrome P450 3A4
JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 12 (4) pp. 2101-2109 (2016)
doi: -
In Silico Design of Short Peptides as Sensing Elements for Phenolic Compounds
ACS SENSORS , 1 (3) pp. 279-286 (2016)
doi: -
Density effects in entangled solutions of linear and ring polymers
JOURNAL OF PHYSICS-CONDENSED MATTER , 28 (6) (2016)
doi: -
The elusive quest for RNA knots
RNA BIOLOGY , 13 (2) pp. 134-139 (2016)
doi:
2015
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Interfacing proteins with graphitic nanomaterials: from spontaneous attraction to tailored assemblies
CHEMICAL SOCIETY REVIEWS , 44 (19) pp. 6916-6953 (2015)
doi: -
Pore Translocation of Knotted Polymer Chains: How Friction Depends on Knot Complexity
ACS MACRO LETTERS , 4 (12) pp. 1420-1424 (2015)
doi: -
Fluctuations of rotational and translational degrees of freedom in an interacting active dumbbell system
CHAOS SOLITONS & FRACTALS , 81 pp. 556-566 (2015)
doi: -
Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations
BMC BIOINFORMATICS , 16 (2015)
doi: -
Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations
NUCLEIC ACIDS RESEARCH , 43 (20) pp. 9626-9644 (2015)
doi: -
Stretching Response of Knotted and Unknotted Polymer Chains
PHYSICAL REVIEW LETTERS , 115 (18) (2015)
doi: -
The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments
SCIENTIFIC REPORTS , 5 (2015)
doi: -
Designing High-Affinity Peptides for Organic Molecules by Explicit Solvent Molecular Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B , 119 (41) pp. 12963-12969 (2015)
doi: -
Role of Water in the Puzzling Mechanism of the Final Aromatization Step Promoted by the Human Aromatase Enzyme. Insights from QM/MM MD Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING , 55 (10) pp. 2218-2226 (2015)
doi: -
QMMMW: A wrapper for QM/MM simulations with QUANTUM ESPRESSO and LAMMPS
COMPUTER PHYSICS COMMUNICATIONS , 195 pp. 191-198 (2015)
doi: -
Integral equation analysis of single-site coarse-grained models for polymer-colloid mixtures
MOLECULAR PHYSICS , 113 (17-18) pp. 2629-2642 (2015)
doi: -
ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations.
NUCLEIC ACIDS RESEARCH , 43 (18) pp. 8725-34 (2015)
doi: -
Designing High-Affinity Peptides for Organic Molecules by Explicit Solvent Molecular Dynamics.
THE JOURNAL OF PHYSICAL CHEMISTRY. B , 119 (41) pp. 12963-9 (2015)
doi: -
QMMMW: A wrapper for QM/MM simulations with QUANTUM ESPRESSO and LAMMPS
COMPUTER PHYSICS COMMUNICATIONS , 195 pp. 191-198 (2015)
doi: -
Knotting dynamics of DNA chains of different length confined in nanochannels.
JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL , 27 (35) pp. 354102-354102 (2015)
doi: -
Molecular Crowding Increases Knots Abundance in Linear Polymers
MACROMOLECULES , 48 (17) pp. 6337-6346 (2015)
doi: -
Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments
NUCLEIC ACIDS RESEARCH , 43 (15) pp. 7260-7269 (2015)
doi: -
Coarse-graining polymer solutions: A critical appraisal of single- and multi-site models
EUROPEAN PHYSICAL JOURNAL-SPECIAL TOPICS , 224 (12) pp. 2239-2267 (2015)
doi: -
SPECTRUS: A Dimensionality Reduction Approach for Identifying Dynamical Domains in Protein Complexes from Limited Structural Datasets
STRUCTURE , 23 (8) pp. 1516-1525 (2015)
doi: -
Rotational and translational diffusion in an interacting active dumbbell system
PHYSICAL REVIEW E , 91 (6) (2015)
doi: -
Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering
JOURNAL OF PHYSICAL CHEMISTRY B , 119 (23) pp. 6941-6951 (2015)
doi: -
QM/MM MD Simulations on the Enzymatic Pathway of the Human Flap Endonuclease (hFEN1) Elucidating Common Cleavage Pathways to RNase H Enzymes
ACS CATALYSIS , 5 (6) pp. 3864-3875 (2015)
doi: -
Ab Initio Study of the Reaction of Ozone with Bromide Ion
JOURNAL OF PHYSICAL CHEMISTRY A , 119 (19) pp. 4482-4488 (2015)
doi: -
Amyloid beta Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies
CHEMICAL REVIEWS , 115 (9) pp. 3518-3563 (2015)
doi: -
Electric Field Controlled Columnar and Planar Patterning of Cholesteric Colloids
PHYSICAL REVIEW LETTERS , 114 (17) (2015)
doi: -
Motility-induced phase separation and coarsening in active matter
COMPTES RENDUS PHYSIQUE , 16 (3) pp. 316-331 (2015)
doi: -
Native fold and docking pose discrimination by the same residue-based scoring function
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , 83 (4) pp. 621-630 (2015)
doi: -
An Efficient Algorithm to Perform Local Concerted Movements of a Chain Molecule
PLOS ONE , 10 (3) (2015)
doi: -
Self-assembling knots of controlled topology by designing the geometry of patchy templates
NATURE COMMUNICATIONS , 6 (2015)
doi: -
Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering
JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 11 (3) pp. 1077-1085 (2015)
doi: -
Absence of knots in known RNA structures
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA , 112 (7) pp. 2052-2057 (2015)
doi: -
Synonymous Mutations Reduce Genome Compactness in Icosahedral ssRNA Viruses
BIOPHYSICAL JOURNAL , 108 (1) pp. 194-202 (2015)
doi: -
Further theoretical insight into the reaction mechanism of the hepatitis C NS3/NS4A serine protease
CHEMICAL PHYSICS LETTERS , 619 pp. 97-102 (2015)
doi: -
Interfacing proteins with graphitic nanomaterials: from spontaneous attraction to tailored assemblies
CHEMICAL SOCIETY REVIEWS , 44 (19) pp. 6916-6953 (2015)
doi: -
The effect of anaesthetics on the properties of a lipid membrane in the biologically relevant phase: a computer simulation study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS , 17 (22) pp. 14750-14760 (2015)
doi: -
Using reweighted pulling simulations to characterize conformational changes in riboswitches.
METHODS IN ENZYMOLOGY , 553 pp. 139-62 (2015)
doi: -
Accurate Multiple Time Step in Biased Molecular Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 11 (1) pp. 139-146 (2015)
doi:
2014
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Accurate coarse-grained models for mixtures of colloids and linear polymers under good-solvent conditions
JOURNAL OF CHEMICAL PHYSICS , 141 (24) (2014)
doi: -
Viscoelasticity of model interphase chromosomes
JOURNAL OF CHEMICAL PHYSICS , 141 (24) (2014)
doi: -
Metadynamics Simulations Reveal a Na+ Independent Exiting Path of Galactose for the Inward-Facing Conformation of vSGLT
PLOS COMPUTATIONAL BIOLOGY , 10 (12) (2014)
doi: -
The role of nucleobase interactions in RNA structure and dynamics
NUCLEIC ACIDS RESEARCH , 42 (21) pp. 13306-13314 (2014)
doi: -
Dynamics of a homogeneous active dumbbell system
PHYSICAL REVIEW E , 90 (5) (2014)
doi: -
Molecular Dynamics Simulations Identify Time Scale of Conformational Changes Responsible for Conformational Selection in Molecular Recognition of HIV-1 Transactivation Responsive RNA
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY , 136 (44) pp. 15631-15637 (2014)
doi: -
Computational Approaches Elucidate the Allosteric Mechanism of Human Aromatase Inhibition: A Novel Possible Route to Small-Molecule Regulation of CYP450s Activities?
JOURNAL OF CHEMICAL INFORMATION AND MODELING , 54 (10) pp. 2856-2868 (2014)
doi: -
Bowl Inversion of Surface-Adsorbed Sumanene
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY , 136 (39) pp. 13666-13671 (2014)
doi: -
Spectroscopic Properties of Benzene at the Air-Ice Interface: A Combined Experimental-Computational Approach
JOURNAL OF PHYSICAL CHEMISTRY A , 118 (35) pp. 7535-7547 (2014)
doi: -
Knotting and Unknotting Dynamics of DNA Strands in Nanochannels
ACS MACRO LETTERS , 3 (9) pp. 876-880 (2014)
doi: -
Atomistic-Level Portrayal of Drug-DNA Interplay: A History of Courtships and Meetings Revealed by Molecular Simulations
CHEMMEDCHEM , 9 (9) pp. 1966-1981 (2014)
doi: -
Ru[(bpy)(2)(dppz)](2+) and Rh[(bpy)(2)(chrysi)](3+) Targeting Double Strand DNA: The Shape of the Intercalating Ligand Tunes the Free Energy Landscape of Deintercalation
INORGANIC CHEMISTRY , 53 (15) pp. 7999-8008 (2014)
doi: -
Phase diagram of mixtures of colloids and polymers in the thermal crossover from good to theta solvent
JOURNAL OF CHEMICAL PHYSICS , 141 (2) (2014)
doi: -
Clustering by fast search and find of density peaks
SCIENCE , 344 (6191) pp. 1492-1496 (2014)
doi: -
Ring Polymers in the Melt State: The Physics of Crumpling
PHYSICAL REVIEW LETTERS , 112 (11) (2014)
doi: -
Shape and area fluctuation effects on nucleation theory
JOURNAL OF CHEMICAL PHYSICS , 140 (9) (2014)
doi: -
Hamiltonian replica exchange in GROMACS: a flexible implementation
MOLECULAR PHYSICS , 112 (3-4) pp. 379-384 (2014)
doi: -
PLUMED 2: New feathers for an old bird
COMPUTER PHYSICS COMMUNICATIONS , 185 (2) pp. 604-613 (2014)
doi: -
Driving knots on DNA with AC/DC electric fields: topological friction and memory effects
SOFT MATTER , 10 (34) pp. 6491-6498 (2014)
doi: -
Computational Models of Large-Scale Genome Architecture
NEW MODELS OF THE CELL NUCLEUS: CROWDING, ENTROPIC FORCES, PHASE SEPARATION, AND FRACTALS , 307 pp. 275-349 (2014)
doi: -
Probing riboswitch binding sites with molecular docking, focused libraries, and in-line probing assays.
METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) , 1103 pp. 141-51 (2014)
doi: -
Calculation of the intrinsic solvation free energy profile of methane across a liquid/liquid interface in computer simulations
JOURNAL OF MOLECULAR LIQUIDS , 189 pp. 39-43 (2014)
doi: -
Role of the fluidity of a liquid phase in determining the surface properties of the opposite phase (Reprinted from Journal of Molecular Liquids, Vol 186, Pages 7-13, 2013)
JOURNAL OF MOLECULAR LIQUIDS , 189 pp. 122-128 (2014)
doi: -
Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
ENTROPY , 16 (1) pp. 163-199 (2014)
doi:
2013
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BACHSCORE. A tool for evaluating efficiently and reliably the quality of large sets of protein structures
COMPUTER PHYSICS COMMUNICATIONS , 184 (12) pp. 2860-2865 (2013)
doi: -
Partial inhibition and bilevel optimization in flux balance analysis
BMC BIOINFORMATICS , 14 (2013)
doi: -
Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition
PLOS COMPUTATIONAL BIOLOGY , 9 (11) (2013)
doi: -
Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch
RNA-A PUBLICATION OF THE RNA SOCIETY , 19 (11) pp. 1517-1524 (2013)
doi: -
Structural and Dynamic Properties of Monoclonal Antibodies Immobilized on CNTs: A Computational Study
CHEMISTRY-A EUROPEAN JOURNAL , 19 (37) pp. 12281-12293 (2013)
doi: -
Time-dependent information transmission in a model regulatory circuit
PHYSICAL REVIEW E , 88 (2) (2013)
doi: -
Functionalized Fe-Filled Multiwalled Carbon Nanotubes as Multifunctional Scaffolds for Magnetization of Cancer Cells
ADVANCED FUNCTIONAL MATERIALS , 23 (25) pp. 3173-3184 (2013)
doi: -
Genome-wide expression profiling and functional characterization of SCA28 lymphoblastoid cell lines reveal impairment in cell growth and activation of apoptotic pathways
BMC MEDICAL GENOMICS , 6 (2013)
doi: -
Structural Role of Uracil DNA Glycosylase for the Recognition of Uracil in DNA Duplexes. Clues from Atomistic Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING , 53 (6) pp. 1371-1387 (2013)
doi: -
Randomness in self-organized phenomena. A case study: Retinal angiogenesis
BIOSYSTEMS , 112 (3) pp. 292-297 (2013)
doi: -
Spontaneous Knotting and Unknotting of Flexible Linear Polymers: Equilibrium and Kinetic Aspects
MACROMOLECULES , 46 (9) pp. 3669-3678 (2013)
doi: -
A rate-distortion theory for gene regulatory networks and its application to logic gate consistency
BIOINFORMATICS , 29 (9) pp. 1166-1173 (2013)
doi: -
Conformational Fluctuations of UreG, an Intrinsically Disordered Enzyme
BIOCHEMISTRY , 52 (17) pp. 2949-2954 (2013)
doi: -
Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA , 110 (17) pp. 6817-6822 (2013)
doi: -
Nucleation Process of a Fibril Precursor in the C-Terminal Segment of Amyloid-beta
PHYSICAL REVIEW LETTERS , 110 (16) (2013)
doi: -
Topological constraints and chromosome organization in eukaryotes: a physical point of view
BIOCHEMICAL SOCIETY TRANSACTIONS , 41 pp. 612-615 (2013)
doi: -
Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field
PLOS COMPUTATIONAL BIOLOGY , 9 (3) (2013)
doi: -
Special issue on physical virology
JOURNAL OF BIOLOGICAL PHYSICS , 39 (2) pp. 161-162 (2013)
doi: -
Knotting of linear DNA in nano-slits and nano-channels: a numerical study
JOURNAL OF BIOLOGICAL PHYSICS , 39 (2) pp. 267-275 (2013)
doi: -
Comparing proteins by their internal dynamics: Exploring structure-function relationships beyond static structural alignments
PHYSICS OF LIFE REVIEWS , 10 (1) pp. 1-26 (2013)
doi: -
Reply to comments on "Comparing proteins by their internal dynamics: Exploring structure-function relationships beyond static structural alignments"
PHYSICS OF LIFE REVIEWS , 10 (1) pp. 39-40 (2013)
doi: -
Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19
PLOS COMPUTATIONAL BIOLOGY , 9 (3) (2013)
doi: -
RNA/Peptide Binding Driven by Electrostatics-Insight from Bidirectional Pulling Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 9 (3) pp. 1720-1730 (2013)
doi: -
A fingerprint of surface-tension anisotropy in the free-energy cost of nucleation
JOURNAL OF CHEMICAL PHYSICS , 138 (6) (2013)
doi: -
Common dynamical features of sensory adaptation in photoreceptors and olfactory sensory neurons
SCIENTIFIC REPORTS , 3 (2013)
doi: -
McGenus: a Monte Carlo algorithm to predict RNA secondary structures with pseudoknots
NUCLEIC ACIDS RESEARCH , 41 (3) pp. 1895-1900 (2013)
doi: -
A Candidate Ion-Retaining State in the Inward-Facing Conformation of Sodium/Galactose Symporter: Clues from Atomistic Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 9 (2) pp. 1240-1246 (2013)
doi:
2012
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Atomistic Structure of Cobalt-Phosphate Nanoparticles for Catalytic Water Oxidation
ACS NANO , 6 (12) pp. 10497-10504 (2012)
doi: -
The role of stochasticity in a model of retinal angiogenesis
IMA JOURNAL OF APPLIED MATHEMATICS , 77 (6) pp. 729-747 (2012)
doi: -
Absolute Transition Rates for Rare Events from Dynamical Decoupling of Reaction Variables
PHYSICAL REVIEW LETTERS , 109 (15) (2012)
doi: -
Exploring the low-energy landscape of large-scale signed social networks
PHYSICAL REVIEW E , 86 (3) (2012)
doi: -
Role of the Subunit Interactions in the Conformational Transitions in Adult Human Hemoglobin: An Explicit Solvent Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B , 116 (36) pp. 11004-11009 (2012)
doi: -
Topological Jamming of Spontaneously Knotted Polyelectrolyte Chains Driven Through a Nanopore
PHYSICAL REVIEW LETTERS , 109 (11) (2012)
doi: -
Predicting and characterizing selective multiple drug treatments for metabolic diseases and cancer
BMC SYSTEMS BIOLOGY , 6 (2012)
doi: -
Effects of the Pathological Q212P Mutation on Human Prion Protein Non-Octarepeat Copper-Binding Site
BIOCHEMISTRY , 51 (31) pp. 6068-6079 (2012)
doi: -
A Novel Approach to the Investigation of Passive Molecular Permeation through Lipid Bilayers from Atomistic Simulations
JOURNAL OF PHYSICAL CHEMISTRY B , 116 (29) pp. 8714-8721 (2012)
doi: -
Metadynamics with Adaptive Gaussians
JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 8 (7) pp. 2247-2254 (2012)
doi: -
The Role of Non-Native Interactions in the Folding of Knotted Proteins
PLOS COMPUTATIONAL BIOLOGY , 8 (6) (2012)
doi: -
Influence of the Membrane Lipophilic Environment on the Structure and on the Substrate Access/Egress Routes of the Human Aromatase Enzyme. A Computational Study
JOURNAL OF CHEMICAL INFORMATION AND MODELING , 52 (6) pp. 1595-1606 (2012)
doi: -
Systematic Improvement of Classical Nucleation Theory
PHYSICAL REVIEW LETTERS , 108 (22) (2012)
doi: -
A simple and efficient statistical potential for scoring ensembles of protein structures
SCIENTIFIC REPORTS , 2 (2012)
doi: -
On the active site of mononuclear B1 metallo beta-lactamases: a computational study
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN , 26 (4) pp. 425-435 (2012)
doi: -
RNA Unwinding from Reweighted Pulling Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY , 134 (11) pp. 5173-5179 (2012)
doi: -
Corresponding Functional Dynamics across the Hsp90 Chaperone Family: Insights from a Multiscale Analysis of MD Simulations
PLOS COMPUTATIONAL BIOLOGY , 8 (3) (2012)
doi: -
Designing Short Peptides with High Affinity for Organic Molecules: A Combined Docking, Molecular Dynamics, And Monte Carlo Approach
JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 8 (3) pp. 1121-1128 (2012)
doi: -
Multidimensional View of Amyloid Fibril Nucleation in Atomistic Detail
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY , 134 (8) pp. 3886-3894 (2012)
doi: -
Numerical Study of Linear and Circular Model DNA Chains Confined in a Slit: Metric and Topological Properties
MACROMOLECULES , 45 (4) pp. 2113-2121 (2012)
doi: -
The Structural Role of Mg2+ Ions in a Class I RNA Polymerase Ribozyme: A Molecular Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY B , 116 (7) pp. 2259-2268 (2012)
doi: -
Detecting DNA Mismatches with Metallo-Insertors: A Molecular Simulation Study
INORGANIC CHEMISTRY , 51 (4) pp. 2046-2057 (2012)
doi: -
A small chemical library of 2-aminoimidazole derivatives as BACE-1 inhibitors: Structure-based design, synthesis, and biological evaluation
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY , 48 pp. 206-213 (2012)
doi: -
Multi-scale modeling of diffusion-controlled reactions in polymers: Renormalisation of reactivity parameters
JOURNAL OF CHEMICAL PHYSICS , 136 (1) (2012)
doi: -
Knotting and metric scaling properties of DNA confined in nano-channels: a Monte Carlo study
SOFT MATTER , 8 (42) pp. 10959-10968 (2012)
doi: -
Hybridization in nanostructured DNA monolayers probed by AFM: theory versus experiment
NANOSCALE , 4 (5) pp. 1734-1741 (2012)
doi: -
METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations
COMPUTER PHYSICS COMMUNICATIONS , 183 (1) pp. 203-211 (2012)
doi:
2011
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Synthesis of Monomeric Derivatives To Probe Memoquin's Bivalent Interactions
JOURNAL OF MEDICINAL CHEMISTRY , 54 (24) pp. 8299-8304 (2011)
doi: -
Structure and Dynamics of Ring Polymers: Entanglement Effects Because of Solution Density and Ring Topology
MACROMOLECULES , 44 (21) pp. 8668-8680 (2011)
doi: -
Theory of the reentrant quantum rotational phase transition in high-pressure HD
PHYSICAL REVIEW B , 84 (14) (2011)
doi: -
Multiscale Entanglement in Ring Polymers under Spherical Confinement
PHYSICAL REVIEW LETTERS , 107 (18) (2011)
doi: -
Conformations of the Huntingtin N-term in aqueous solution from atomistic simulations
FEBS LETTERS , 585 (19) pp. 3086-3089 (2011)
doi: -
Nonkinetic Modeling of the Mechanical Unfolding of Multimodular Proteins: Theory and Experiments
BIOPHYSICAL JOURNAL , 101 (6) pp. 1504-1512 (2011)
doi: -
Reactive force field simulation of proton diffusion in BaZrO3 using an empirical valence bond approach
JOURNAL OF PHYSICS-CONDENSED MATTER , 23 (33) (2011)
doi: -
Cytoskeletal actin networks in motile cells are critically self-organized systems synchronized by mechanical interactions
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA , 108 (34) pp. 13978-13983 (2011)
doi: -
Polymers with spatial or topological constraints: Theoretical and computational results
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS , 504 (1) pp. 1-73 (2011)
doi: -
SiO2 in density functional theory and beyond
PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS , 248 (5) pp. 1061-1066 (2011)
doi: -
Sequential Virtual Screening Approach to the Identification of Small Organic Molecules as Potential BACE-1 Inhibitors
CHEMICAL BIOLOGY & DRUG DESIGN , 77 (4) pp. 268-271 (2011)
doi: -
Finite Temperature Properties of Clusters by Replica Exchange Metadynamics: The Water Nonamer
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY , 133 (8) pp. 2535-2540 (2011)
doi: -
Bridging the Atomic and Coarse-Grained Descriptions of Collective Motions in Proteins
MULTISCALE APPROACHES TO PROTEIN MODELING , pp. 159-178 (2011)
doi: -
Theoretical Studies of Homogeneous Catalysts Mimicking Nitrogenase
MOLECULES , 16 (1) pp. 442-465 (2011)
doi: -
Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?
PHYSICAL CHEMISTRY CHEMICAL PHYSICS , 13 (22) pp. 10421-10425 (2011)
doi: -
Initial stages of salt crystal dissolution determined with ab initio molecular dynamics
PHYSICAL CHEMISTRY CHEMICAL PHYSICS , 13 (29) pp. 13162-13166 (2011)
doi: