| 8335 - 8336 |
Macromolecular Systems Understood through Multiscale and Enhanced Sampling Techniques Preface
Ortoleva PJ, Keyes T, Tuckerman M |
| 8337 - 8349 |
Coarse-Grained Modeling of Simple Molecules at Different Resolutions in the Absence of Good Sampling
Larini L, Shea JE |
| 8350 - 8354 |
Molecular Dynamics in Principal Component Space
Michielssens S, van Erp TS, Kutzner C, Ceulemans A, de Groot BL |
| 8355 - 8362 |
Nanosystem Self-Assembly Pathways Discovered via All-Atom Multiscale Analysis
Pankavich SD, Ortoleva PJ |
| 8363 - 8374 |
Optimal Number of Coarse-Grained Sites in Different Components of Large Biomolecular Complexes
Sinitskiy AV, Saunders MG, Voth GA |
| 8375 - 8382 |
Discrete Molecular Dynamics: An Efficient And Versatile Simulation Method For Fine Protein Characterization
Shirvanyants D, Ding F, Tsao D, Ramachandran S, Dokholyan NV |
| 8383 - 8393 |
A New Multiscale Algorithm and Its Application to Coarse-Grained Peptide Models for Self-Assembly
Carmichael SP, Shell MS |
| 8394 - 8411 |
Evolution of the Potential Energy Landscape with Static Pulling Force for Two Model Proteins
Wales DJ, Head-Gordon T |
| 8412 - 8422 |
Structures of A beta 17-42 Trimers in Isolation and with Five Small-Molecule Drugs Using a Hierarchical Computational Procedure
Chebaro Y, Jiang P, Zang T, Mu YG, Nguyen PH, Mousseau N, Derreumaux P |
| 8423 - 8434 |
Space Warping Order Parameters and Symmetry: Application to Multiscale Simulation of Macromolecular Assemblies
Singharoy A, Joshi H, Miao YL, Ortoleva PJ |
| 8435 - 8448 |
Statistics of Multiscale Fluctuations in Macromolecular Systems
Yukalov VI, Yukalova EP |
| 8449 - 8459 |
Dynamics and Calcium Association to the N-Terminal Regulatory Domain of Human Cardiac Troponin C: A Multiscale Computational Study
Lindert S, Kekenes-Huskey PM, Huber G, Pierce L, McCammon JA |
| 8460 - 8473 |
Multiscale Simulation on a Light-Harvesting Molecular Triad
Su GX, Czader A, Homouz D, Bernardes G, Mateen S, Cheung MS |
| 8474 - 8484 |
Derivation of Coarse Grained Models for Multiscale Simulation of Liquid Crystalline Phase Transitions
Mukherjee B, Delle Site L, Kremer K, Peter C |
| 8485 - 8493 |
Multiscale Simulations of the Antimicrobial Peptide Maculatin 1.1: Water Permeation through Disordered Aggregates
Parton DL, Akhmatskaya EV, Sansom MSP |
| 8494 - 8503 |
AWSEM-MD: Protein Structure Prediction Using Coarse-Grained Physical Potentials and Bioinformatically Based Local Structure Biasing
Davtyan A, Schafer NP, Zheng WH, Clementi C, Wolynes PG, Papoian GA |
| 8504 - 8512 |
Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution
Nishima W, Miyashita N, Yamaguchi Y, Sugita Y, Re S |
| 8513 - 8522 |
Influence of the Shape of Crowding Particles on the Structural Transitions in a Polymer
Kudlay A, Cheung MS, Thirumalai D |
| 8523 - 8533 |
Atomic Detail Brownian Dynamics Simulations of Concentrated Protein Solutions with a Mean Field Treatment of Hydrodynamic Interactions
Mereghetti P, Wade RC |
| 8534 - 8544 |
Discovering Free Energy Basins for Macromolecular Systems via Guided Multiscale Simulation
Sereda YV, Singharoy AB, Jarrold MF, Ortoleva PJ |
| 8545 - 8555 |
Multiscale Modeling of the Nanomechanics of Microtubule Protofilaments
Theisen KE, Zhmurov A, Newberry ME, Barsegov V, Dima RI |
| 8556 - 8572 |
Multiscale Modeling of Double-Helical DNA and RNA: A Unification through Lie Groups
Wolfe KC, Hastings WA, Dutta S, Long A, Shapiro BA, Woolf TB, Guthold M, Chirikjian GS |
| 8573 - 8583 |
Characterization of a Dynamic String Method for the Construction of Transition Pathways in Molecular Reactions
Johnson ME, Hummer G |
| 8584 - 8603 |
Analysis and Elimination of a Bias in Targeted Molecular Dynamics Simulations of Conformational Transitions: Application to Calmodulin
Ovchinnikov V, Karplus M |
| 8604 - 8609 |
On the Morphology of Viral Capsids: Elastic Properties and Buckling Transitions
May ER, Brooks CL |
| 8610 - 8620 |
Conformational Sampling of Peptides in the Presence of Protein Crowders from AA/CG-Multiscale Simulations
Predeus AV, Gul S, Gopal SM, Feig M |
| 8621 - 8635 |
The Role of Many-Body Correlations in Determining Potentials for Coarse-Grained Models of Equilibrium Structure
Rudzinski JF, Noid WG |
| 8636 - 8645 |
fSUB: Normal Mode Analysis with Flexible Substructures
Lu MY, Ming DM, Ma JP |
| 8646 - 8653 |
Replica Exchange Statistical Temperature Molecular Dynamics Algorithm
Kim J, Straub JE, Keyes T |
| 8654 - 8661 |
Exploring the Solid-Liquid Phase Change of an Adapted Dzugutov Model Using Generalized Replica Exchange Method
Lu Q, Kim J, Straub JE |
| 8662 - 8691 |
Early Events in Helix Unfolding under External Forces: A Milestoning Analysis
Kreuzer SM, Elber R, Moon TJ |
| 8692 - 8702 |
The Shadow Map: A General Contact Definition for Capturing the Dynamics of Biomolecular Folding and Function
Noel JK, Whitford PC, Onuchic JN |
| 8703 - 8713 |
Tracking Polypeptide Folds on the Free Energy Surface: Effects of the Chain Length and Sequence
Brukhno AV, Ricchiuto P, Auer S |
| 8714 - 8721 |
A Novel Approach to the Investigation of Passive Molecular Permeation through Lipid Bilayers from Atomistic Simulations
Ghaemi Z, Minozzi M, Carloni P, Laio A |
| 8722 - 8731 |
A Comparison of Multiscale Methods for the Analysis of Molecular Dynamics Simulations
Benson NC, Daggett V |
