The design of high affinity human PD-1 mutants by using molecular dynamics simulations (MD)

Development of MD Engine: High-speed accelerator with parallel processor design for molecular dynamics simulations

SHINJIRO TOYODA, HIROH MIYAGAWA, KUNIHIRO KITAMURA, TAKASHI AMISAKI, EIRI HASHIMOTO, HITOSHI IKEDA, AKIHIRO KUSUMI, NOBUAKI MIYAKAWA Component Development Department, Suzuka Fuji Xerox Co., Ltd., 2274 Hongo, Ebina, Kanagawa 243-04, Japan Research Center, Taisho Pharmaceutical Co., Ltd., 1-403 Yoshino, Ohmiya, Saitama 330, Japan Department of Mathematics and Computer Science, Shimane University,...

Modeling Nanocomposites for Molecular Dynamics (md) Simulations

Prediction of Functional Loss of Human Angiogenin Mutants Associated with ALS by Molecular Dynamics Simulations

Several missense mutations in the coding region of angiogenin (ANG) gene have been identified in Amyotrophic Lateral Sclerosis (ALS) patients. These mutations lead to loss of either ribonucleolytic activity or nuclear translocation activity or both of ANG (protein encoded by ANG gene) causing ALS. We present here a cohesive and comprehensive picture of the molecular origins of functional loss o...

Molecular Dynamics Simulations of Freezing Behavior of Pure Water and 14% Water-NaCl Mixture Using the Coarse-Grained Model

 We performed molecular dynamics simulations using the coarse-grained model to study the freezing behavior of pure water and 14% water-salt mixture in a wide range of temperatures for a very long time around 50 nanoseconds. For the salty water, an interface in nanoscale was used. For both systems, the f...

Size Dependence of the Elastic Properties of Pd Nanowire: Molecular Dynamics Simulation

The mechanical properties including elastic stiffness constants as well as bulk modulus of Palladium (Pd) nanowire were calculated in the constant temperature and pressure (NPT), ensemble by molecular dynamics (MD) simulation technique. The quantum Sutton-Chen (Q-SC) many-body potential was used to calculate the cohesive energy as well as forces experience by every atoms. The temperature and pr...