Extracting Realistic Kinetics of Rare Activated Processes from Accelerated Molecular Dynamics Using Kramers’ Theory

2011 ◽  
Vol 7 (3) ◽  
pp. 575-581 ◽  
Author(s):  
Urmi Doshi ◽  
Donald Hamelberg
Keyword(s):  
Molecular Dynamics ◽  
Accelerated Molecular Dynamics ◽  
Activated Processes ◽  
Kinetics Of

scholarly journals The effects of cation–anion clustering on defect migration in MgAl2O4

2016 ◽  
Vol 18 (29) ◽  
pp. 19647-19654 ◽  
Author(s):  
Richard J. Zamora ◽  
Arthur F. Voter ◽  
Danny Perez ◽  
Romain Perriot ◽  
Blas P. Uberuaga
Keyword(s):  
Molecular Dynamics ◽  
Lattice Defects ◽  
Magnesium Aluminate ◽  
Magnesium Aluminate Spinel ◽  
Defect Migration ◽  
Accelerated Molecular Dynamics ◽  
Kinetics Of

Magnesium aluminate spinel offers a range of exciting technological applications. We use accelerated molecular dynamics to illuminate new details about the kinetics of relevant lattice defects.

scholarly journals Morphology, energetics and growth kinetics of diphenylalanine fibres

2021 ◽  
Author(s):  
Phillip Mark Rodger ◽  
Caroline Montgomery ◽  
Giovanni Costantini ◽  
Alison Rodger
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Growth Kinetics ◽  
Dynamics Simulations ◽  
Kinetics Of

The formation and stability of diphenylalanine fibres are studied by combining molecular dynamics simulations with microscopy and spectroscopy experiments, quantitatively detailing their morphology, energetics and growth kinetics.

Dynamics and kinetics of the Si(1D) + H2/D2 reactions on a new global ab initio potential energy surface

2021 ◽  
Vol 23 (10) ◽  
pp. 6141-6153
Author(s):  
Jianwei Cao ◽  
Yanan Wu ◽  
Haitao Ma ◽  
Zhitao Shen ◽  
Wensheng Bian
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Quantum Dynamics ◽  
Energy Surface ◽  
Molecular Dynamics Calculations ◽  
Ring Polymer ◽  
Ring Polymer Molecular Dynamics ◽  
Kinetics Of

Quantum dynamics and ring polymer molecular dynamics calculations reveal interesting dynamical and kinetic behaviors of an endothermic complex-forming reaction.

scholarly journals Anti-TNF Alpha Antibody Humira with pH-dependent Binding Characteristics: A constant-pH Molecular Dynamics, Gaussian Accelerated Molecular Dynamics, and In Vitro Study

Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 334
Author(s):  
Shih-Ting Hong ◽  
Yu-Cheng Su ◽  
Yu-Jen Wang ◽  
Tian-Lu Cheng ◽  
Yeng-Tseng Wang
Keyword(s):  
Molecular Dynamics ◽  
Tnf Alpha ◽  
Complex Structures ◽  
Binding Characteristics ◽  
Accelerated Molecular Dynamics ◽  
Constant Ph ◽  
Ph Dependent ◽  
Constant Ph Molecular Dynamics ◽  
Antibody Drug

Humira is a monoclonal antibody that binds to TNF alpha, inactivates TNF alpha receptors, and inhibits inflammation. Neonatal Fc receptors can mediate the transcytosis of Humira–TNF alpha complex structures and process them toward degradation pathways, which reduces the therapeutic effect of Humira. Allowing the Humira–TNF alpha complex structures to dissociate to Humira and soluble TNF alpha in the early endosome to enable Humira recycling is crucial. We used the cytoplasmic pH (7.4), the early endosomal pH (6.0), and pKa of histidine side chains (6.0–6.4) to mutate the residues of complementarity-determining regions with histidine. Our engineered Humira (W1-Humira) can bind to TNF alpha in plasma at neutral pH and dissociate from the TNF alpha in the endosome at acidic pH. We used the constant-pH molecular dynamics, Gaussian accelerated molecular dynamics, two-dimensional potential mean force profiles, and in vitro methods to investigate the characteristics of W1-Humira. Our results revealed that the proposed Humira can bind TNF alpha with pH-dependent affinity in vitro. The W1-Humira was weaker than wild-type Humira at neutral pH in vitro, and our prediction results were close to the in vitro results. Furthermore, our approach displayed a high accuracy in antibody pH-dependent binding characteristics prediction, which may facilitate antibody drug design. Advancements in computational methods and computing power may further aid in addressing the challenges in antibody drug design.

GPU-accelerated molecular dynamics: State-of-art software performance and porting from Nvidia CUDA to AMD HIP

2021 ◽  
pp. 109434202110082
Author(s):  
Nikolay Kondratyuk ◽  
Vsevolod Nikolskiy ◽  
Daniil Pavlov ◽  
Vladimir Stegailov
Keyword(s):  
Molecular Dynamics ◽  
High Performance ◽  
Software Performance ◽  
Computing Systems ◽  
Accelerated Molecular Dynamics ◽  
Nvidia Cuda ◽  
Software And Hardware ◽  
Management Capabilities ◽  
Utilization Time ◽  
Performance Computing

Classical molecular dynamics (MD) calculations represent a significant part of the utilization time of high-performance computing systems. As usual, the efficiency of such calculations is based on an interplay of software and hardware that are nowadays moving to hybrid GPU-based technologies. Several well-developed open-source MD codes focused on GPUs differ both in their data management capabilities and in performance. In this work, we analyze the performance of LAMMPS, GROMACS and OpenMM MD packages with different GPU backends on Nvidia Volta and AMD Vega20 GPUs. We consider the efficiency of solving two identical MD models (generic for material science and biomolecular studies) using different software and hardware combinations. We describe our experience in porting the CUDA backend of LAMMPS to ROCm HIP that shows considerable benefits for AMD GPUs comparatively to the OpenCL backend.

Sign in / Sign up

Export Citation Format

Share Document