All Stories

  1. Extension of the Einstein molecule method for solid free energy calculation to non-periodic and semi-periodic systems
  2. A hybrid, bottom-up, structurally accurate, Go¯-like coarse-grained protein model
  3. Modelling and simulation of DNA-mediated self-assembly for superlattice design
  4. Free Energy Surface of an Intrinsically Disordered Protein: Comparison between Temperature Replica Exchange Molecular Dynamics and Bias-Exchange Metadynamics
  5. Folding thermodynamics ofβ-hairpins studied by replica-exchange molecular dynamics simulations
  6. Computational study of trimer self-assembly and fluid phase behavior
  7. Correction to Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association
  8. Equilibrium and nonequilibrium dynamics of soft sphere fluids
  9. Thermodynamics and Kinetics of Multi-Protein Binding in Crowded Environments
  10. Molecular Simulations of Unfolded and Intrinsically Disordered Proteins
  11. Membrane Cholesterol Association and Structure of Two Leukotoxin Peptides
  12. Optimized Force Fields for Simulations of Intrinsically Disordered Proteins
  13. Comparing Solution Structures of Amylin and CGRP by Nanosecond Laser-Pump Spectroscopy and Atomistic Simulations
  14. Role of solvation in pressure-induced helix stabilization
  15. Disorder in Cholesterol-Binding Functionality of CRAC Peptides: A Molecular Dynamics Study
  16. Insights into DNA-mediated interparticle interactions from a coarse-grained model
  17. Water transport through functionalized nanotubes with tunable hydrophobicity
  18. Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association
  19. Macromolecular Crowding Effects on Coupled Folding and Binding
  20. Modest Influence of FRET Chromophores on the Properties of Unfolded Proteins
  21. Interaction of Single-Stranded DNA with Curved Carbon Nanotube Is Much Stronger Than with Flat Graphite
  22. Correction to “Molecular Simulations Indicate Marked Differences in the Structure of Amylin Mutants, Correlated with Known Aggregation Propensity”
  23. Effect of molecular structure on fluid transport through carbon nanotubes
  24. Binding between DNA and Carbon Nanotubes Strongly Depends upon Sequence and Chirality
  25. Correlation of Helical Propensity in Amylin Sequences with Known Aggregation Propensity
  26. Molecular Simulations Indicate Marked Differences in the Structure of Amylin Mutants, Correlated with Known Aggregation Propensity
  27. Structural Stability and Binding Strength of a Designed Peptide–Carbon Nanotube Hybrid
  28. Ab Initio Crystallization of Alkanes: Structure and Kinetics of Nuclei Formation
  29. Folding free energy surfaces of three small proteins under crowding: validation of the postprocessing method by direct simulation
  30. Crowding Induced Entropy-Enthalpy Compensation in Protein Association Equilibria
  31. Protein–protein interactions in a crowded environment
  32. Folding Kinetics and Unfolded State Dynamics of the GB1 Hairpin from Molecular Simulation
  33. Structural Ensemble of an Intrinsically Disordered Polypeptide
  34. Structural Characteristics of Oligomeric DNA Strands Adsorbed onto Single-Walled Carbon Nanotubes
  35. DNA Base Dimers Are Stabilized by Hydrogen-Bonding Interactions Including Non-Watson–Crick Pairing Near Graphite Surfaces
  36. Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles
  37. Inclusion of Many-Body Effects in the Additive CHARMM Protein CMAP Potential Results in Enhanced Cooperativity of α-Helix and β-Hairpin Formation
  38. Smoothing of the GB1 Hairpin Folding Landscape by Interfacial Confinement
  39. Pair diffusion, hydrodynamic interactions, and available volume in dense fluids
  40. Molecular-Basis of Single-Walled Carbon Nanotube Recognition by Single-Stranded DNA
  41. Residue-Specific α-Helix Propensities from Molecular Simulation
  42. Quantitative Theory for Protein-Protein Interactions in a Crowded Environment
  43. Water Transport through Nanotubes with Varying Interaction Strength between Tube Wall and Water
  44. Sequence-Specific Self-Stitching Motif of Short Single-Stranded DNA on a Single-Walled Carbon Nanotube
  45. Modest Protein−Crowder Attractive Interactions Can Counteract Enhancement of Protein Association by Intermolecular Excluded Volume Interactions
  46. Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences
  47. Macromolecular Crowding Effects on Multiprotein Binding Equilibria: Molecular Simulation and Theory
  48. Bind’NGO: Flexible Docking Model for Multiprotein Complexes with Intrinsically Disordered Segments
  49. Macromolecular crowding effects on protein–protein binding affinity and specificity
  50. Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse
  51. Tackling Force-Field Bias in Protein Folding Simulations: Folding of Villin HP35 and Pin WW Domains in Explicit Water
  52. Balance between α and β Structures in Ab Initio Protein Folding
  53. Erratum: “Relationship between thermodynamics and dynamics of supercooled liquids” [J. Chem. Phys. 125, 076102 (2006)]
  54. Interfacial thermodynamics of confined water near molecularly rough surfaces
  55. Replica Exchange Simulations For Macromolecular Crowding Effects on Multiprotein Binding
  56. Dependence of Protein Folding Stability and Dynamics on the Density and Composition of Macromolecular Crowders
  57. Protein Folding Landscapes for Alpha- and Beta-Miniproteins Using All-Atom Simulations with an Optimized Force-Field
  58. Using Compressibility Factor as a Predictor of Confined Hard-Sphere Fluid Dynamics †
  59. Available states and available space: static properties that predict self-diffusivity of confined fluids
  60. Anomalous structure and dynamics of the Gaussian-core fluid
  61. Layering and Position-Dependent Diffusive Dynamics of Confined Fluids
  62. Structural anomalies of fluids: Origins in second and higher coordination shells
  63. Confinement, entropy, and single-particle dynamics of equilibrium hard-sphere mixtures
  64. Relationships between Self-Diffusivity, Packing Fraction, and Excess Entropy in Simple Bulk and Confined Fluids
  65. How short-range attractions impact the structural order, self-diffusivity, and viscosity of a fluid
  66. Does confining the hard-sphere fluid between hard walls change its average properties?
  67. Erratum: “Excess-entropy-based anomalies for a waterlike fluid” [J. Chem. Phys. 125, 244502 (2006)]
  68. Quantitative Link between Single-Particle Dynamics and Static Structure of Supercooled Liquids
  69. Excess-entropy-based anomalies for a waterlike fluid
  70. Using available volume to predict fluid diffusivity in random media
  71. Quantitative Link between Single-Particle Dynamics and Static Structure of Supercooled Liquids
  72. Relationship between thermodynamics and dynamics of supercooled liquids
  73. Thermodynamics Predicts How Confinement Modifies the Dynamics of the Equilibrium Hard-Sphere Fluid
  74. Using Energy Landscapes To Predict the Properties of Thin Films †
  75. Erratum: Instability of Thin Liquid Films by Density Variations: A New Mechanism that Mimics Spinodal Dewetting [Phys. Rev. Lett.PRLTAO0031-9007 89 , 186101 (2002)]
  76. Instability and Dewetting of Thin Films Induced by Density Variations
  77. Instability of Thin Liquid Films by Density Variations: A New Mechanism that Mimics Spinodal Dewetting
  78. Computing Free Volume, Structural Order, and Entropy of Liquids and Glasses