화학공학소재연구정보센터

Journal of Physical Chemistry B

Journal of Physical Chemistry B, Vol.120, No.33 Entire volume, number list
ISSN: 1520-6106 (Print) 

In this Issue (62 articles)

8055 - 8056 Tribute to J. Andrew McCammon
Amaro RE, Madura JD, Wong CF
8057 - 8060 Autobiography of J. Andrew McCammon
McCammon JA
8071 - 8079 Electrophoretic Mobility of a Dilute, Highly Charged "Soft" Spherical Particle in a Charged Hydrogel
Allison S, Li F, Le M
8080 - 8089 Reversible Stochastically Gated Diffusion-Influenced Reactions
Gopich IV, Szabo A
8090 - 8101 Folding PDZ2 Domain Using the Molecular Transfer Model
Liu ZX, Reddy G, Thirumalai D
8102 - 8114 Hydration Properties and Solvent Effects for All-Atom Solutes in Polarizable Coarse-Grained Water
Yan XC, Tirado-Rives J, Jorgensen WL
8115 - 8126 Multi-Conformation Monte Carlo: A Method for Introducing Flexibility in Efficient Simulations of Many-Protein Systems
Prytkova V, Heyden M, Khago D, Freites JA, Butts CT, Martin RW, Tobias DJ
8127 - 8136 Solvent Fluctuations Induce Non-Markovian Kinetics in Hydrophobic Pocket-Ligand Binding
Weiss RG, Setny P, Dzubiella J
8137 - 8146 Recognition of Poly-Ubiquitins by the Proteasome through Protein Refolding Guided by Electrostatic and Hydrophobic Interactions
Zhang Y, Vukovic L, Rudack T, Han W, Schulten K
8147 - 8153 Charged Substrate and Product Together Contribute Like a Nonreactive Species to the Overall Electrostatic Steering in Diffusion-Reaction Processes
Xu JJ, Xie Y, Lu BZ, Zhang LB
8154 - 8163 Free Energy Landscape of Lipid Interactions with Regulatory Binding Sites on the Transmembrane Domain of the EGF Receptor
Hedger G, Shorthouse D, Koldso H, Sansom MSP
8164 - 8174 Fast Method for Computing Chemical Potentials and Liquid Liquid Phase Equilibria of Macromolecular Solutions
Qin SB, Zhou HX
8175 - 8185 HCN, Formamidic Acid, and Formamide in Aqueous Solution: A Free Energy Map
Kua J, Thrush KL
8186 - 8192 Mechanism of pKID/KIX Association Studied by Molecular Dynamics Free Energy Simulations
Bomblies R, Luitz MP, Zacharias M
8193 - 8207 Contribution of Electrostatics to the Kinetics of Electron Transfer from NADH-Cytochrome b(5) Reductase to Fe(III)-Cytochrome b(5)
Kollipara S, Tatireddy S, Pathirathne T, Rathnayake LK, Northrup SH
8208 - 8216 Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning
Cardenas AE, Elber R
8217 - 8229 Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization
Miller MS, Lay WK, Elcock AH
8230 - 8237 Solute-Solvent Energetics Based on Proximal Distribution Functions
Ou SC, Pettitt BM
8238 - 8253 Effects of Cardiac Troponin I Mutation P83S on Contractile Properties and the Modulation by PKA-Mediated Phosphorylation
Cheng YH, Lindert S, Oxenford L, Tu AY, McCulloch AD, Regnier M
8254 - 8263 Mechanism of Inhibition of Cholesteryl Ester Transfer Protein by Small Molecule Inhibitors
Chirasani VR, Sankar R, Senapati S
8264 - 8275 Molecular Effects of cTnC DCM Mutations on Calcium Sensitivity and Myofilament Activation-An Integrated Multiscale Modeling Study
Dewan S, McCabe KJ, Regnier M, McCulloch AD, Lindert S
8276 - 8288 Rapid Characterization of Allosteric Networks with Ensemble Normal Mode Analysis
Yao XQ, Skjaerven L, Grant BJ
8289 - 8301 Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit
Zhang BW, Dai W, Gallicchio E, He P, Xia JC, Tan ZQ, Levy RM
8302 - 8312 The "Lid" in the Streptococcus pneumoniae SrtC1 Sortase Adopts a Rigid Structure that Regulates Substrate Access to the Active Site
Jacobitz AW, Naziga EB, Yi SW, McConnell SA, Peterson R, Jung ME, Clubb RT, Wereszczynski J
8313 - 8320 Picosecond to Millisecond Structural Dynamics in Human Ubiquitin
Lindorff-Larsen K, Maragakis P, Piana S, Shaw DE
8321 - 8337 Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches
Mills JD, Ben-Nun M, Rollin K, Bromley MWJ, Li JB, Hinde RJ, Winstead CL, Sheehy JA, Boatz JA, Langhoff PW
8338 - 8345 The Promiscuity of Allosteric Regulation of Nuclear Receptors by Retinoid X Receptor
Clark AK, Wilder JH, Grayson AW, Johnson QR, Lindsay RJ, Nellas RB, Fernandez EJ, Shen TY
8346 - 8353 Computational Modeling of Competitive Metabolism between omega 3-and omega 6-Polyunsaturated Fatty Acids in Inflammatory Macrophages
Gupta S, Kihara Y, Maurya MR, Norris PC, Dennis EA, Subramanian S
8354 - 8360 Energy Minimization of Discrete Protein Titration State Models Using Graph Theory
Purvine E, Monson K, Jurrus E, Star K, Baker NA
8361 - 8368 Structure and Dynamics Study of LeuT Using the Markov State Model and Perturbation Response Scanning Reveals Distinct Ion Induced Conformational States
Asciutto EK, Gedeon PC, General IJ, Madura JD
8369 - 8378 Scanning of 16S Ribosomal RNA for Peptide Nucleic Acid Targets
Gorska A, Markowska-Zagrajek A, Rownicki M, Trylska J
8379 - 8388 Secondary Interaction Interfaces with PCNA Control Conformational Switching of DNA Polymerase PoIB from Polymerization to Editing
Xu XJ, Yan CL, Kossmann BR, Ivanov I
8389 - 8404 Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II
Taraphder S, Maupin CM, Swanson JMJ, Voth GA
8405 - 8415 Coupled Dynamics and Entropic Contribution to the Allosteric Mechanism of Pin1
Barman A, Hamelberg D
8416 - 8423 Electrostatic Steering Accelerates C3d:CR2 Association
Mohan RR, Huber GA, Morikis D
8424 - 8437 Ionic Hydrogen Bonds and Lipid Packing Defects Determine the Binding Orientation and Insertion Depth of RecA on Multicomponent Lipid Bilayers
Zhang LL, Rajendram M, Weibel DB, Yethiraj A, Cui Q
8438 - 8448 Behavior of Bilayer Leaflets in Asymmetric Model Membranes: Atomistic Simulation Studies
Tian JH, Nickels J, Katsaras J, Cheng XL
8449 - 8456 Transitions of Double-Stranded DNA Between the A- and B-Forms
Waters JT, Lu XJ, Galindo-Murillo R, Gumbart JC, Kim HD, Cheatham TE, Harvey SC
8457 - 8472 A Simple and Accurate Method To Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes
Ovchinnikov V, Nam K, Karplus M
8473 - 8484 Spatial Heat Maps from Fast Information Matching of Fast and Slow Degrees of Freedom: Application to Molecular Dynamics Simulations
Kovacs JA, Wriggers W
8485 - 8517 Origin of Asymmetric Solvation Effects for Ions in Water and Organic Solvents Investigated Using Molecular Dynamics Simulations: The Swain Acity-Basity Scale Revisited
Reif MM, Hunenberger PH
8518 - 8531 Analysis of Ligand-Receptor Association and Intermediate Transfer Rates in Multienzyme Nanostructures with All-Atom Brownian Dynamics Simulations
Roberts CC, Chang CEA
8532 - 8538 PEST Control of Molecular Stripping of NF kappa B from DNA Transcription Sites
Potoyan DA, Zheng WH, Ferreiro DU, Wolynes PG, Komives EA
8539 - 8546 Exploring Electrostatic Effects on the Hydrogen Bond Network of Liquid Water through Many-Body Molecular Dynamics
Straight SC, Paesani F
8547 - 8556 Computational Equilibrium Thermodynamic and Kinetic Analysis of K-Ras Dimerization through an Effector Binding Surface Suggests Limited Functional Role
Sayyed-Ahmad A, Cho KJ, Hancock JF, Gorfe AA
8557 - 8565 Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model
Chen MC, Lin XC, Zheng WH, Onuchic JN, Wolynes PG
8566 - 8570 Parameter-Free Hydrogen-Bond Definition to Classify Protein Secondary Structure
Haghighi H, Higham J, Henchman RH
8571 - 8579 Optimization of Analytical Potentials for Coarse-Grained Biopolymer Models
Mereghetti P, Maccari G, Spampinato GLB, Tozzini V
8580 - 8589 Identification of an Electrostatic Ruler Motif for Sequence-Specific Binding of Collagenase to Collagen
Subramanian SR, Singam ERA, Berinski M, Subramanian V, Wade RC
8590 - 8599 Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk-Deletion Mutants
Durrant JD, Bush RM, Amaro RE
8600 - 8605 Reaction Coordinate-Free Approach to Recovering Kinetics from Potential-Scaled Simulations: Application of Kramers' Rate Theory
Frank AT, Andricioaei I
8606 - 8616 Two Relations to Estimate Membrane Permeability Using Milestoning
Votapka LW, Lee CT, Amaro RE
8617 - 8630 Understanding Ion Binding Affinity and Selectivity in beta-Parvalbumin Using Molecular Dynamics and Mean Spherical Approximation Theory
Kucharski AN, Scott CE, Davis JP, Kekenes-Huskey PM
8631 - 8641 Behavior of P85 and P188 Poloxamer Molecules: Computer Simulations Using United-Atom Force-Field
Goliaei A, Lau EY, Adhikari U, Schwegler E, Berkowitz ML
8642 - 8653 Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements
Bascom GD, Sanbonmatsu KY, Schlick T
8654 - 8667 Claws, Disorder, and Conformational Dynamics of the C-Terminal Region of Human Desmoplakin
McAnany CE, Mura C
8668 - 8684 Evaluation of Representations and Response Models for Polarizable Force Fields
Li A, Voronin A, Fenley AT, Gilson MK
8685 - 8695 Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems
Ghanakota P, Carlson HA
8696 - 8706 Quantifying the Influence of the Crowded Cytoplasm on Small Molecule Diffusion
Kekenes-Huskey PM, Scott CE, Atalay S
8707 - 8721 Charge Central Interpretation of the Full Nonlinear PB Equation: Implications for Accurate and Scalable Modeling of Solvation Interactions
Xiao L, Wang CH, Ye X, Luo R
8722 - 8732 Divergent Diffusion Coefficients in Simulations of Fluids and Lipid Membranes
Vogele M, Hummer G
8733 - 8742 Leveraging the Information from Markov State Models To Improve the Convergence of Umbrella Sampling Simulations
Jo S, Suh D, He ZW, Chipot C, Roux B