Applications of a Single Molecule Theory of Protein Dynamics

A single molecule theory for protein dynamics has been developed since 2012. It consists of the concepts of conformational Gibbs free energy function (CGF) and single molecule thermodynamic hypothesis (STH) that claims that all stable conformations are (local or global) minimizers of CGF. These are enough to give a unified explanations and mechanisms to many aspects of protein dynamics such as protein folding;allostery;denaturation;and intrinsically disordered proteins. Formulas of CGF in water environment had been derived via quantum statistics. Applications of them to soluble proteins are: docking Gibbs free energy difference formula and a practical way to search better docking site;single molecule binding affinity;predicting and explaining why structures of a monomeric globular protein looks like a globule and is tightly packed with a hydrophobic core;a representation of the hydrophobic effect;and a wholistic view to structures of water soluble proteins.

GENERALIZED NOETHER’S THEOREM OF NONHOLONOMIC NONPOTENTIAL SYSTEM IN NONINERTIAL REFERENCE FRAMES

The new Lagrangian of the relative motion of mechanical system is constructed, the varialional principles oj Jourdain's form of nonlinear nonlwlonomic nonpotential system in noninertial reference frame are established, the generalized Noether's theorem of the system above is presented and proved, and the conserved quantities of system are studied.

Goal-Setting in the Information-Generating Environment of the Universe

Problem of goal-setting is related to the fundamental principles of informationology and general, rather than specific, aproaches, which enable a more adequate appraisal of certain managerial decisions in terms of their efficiency. In article this problem is considered and from positions of informationology is formulated and on the basis of a method of full mathematical induction the Law of positive dynamics of the Universe is proved. This law establishes preference of the positive purposes in all processes happening in the Universe. Thus, the goal-setting which is carried out from positions of the described Law is the important world outlook prerequisite searching, identification and development of strategic alternatives of purposeful social innovations.

Effect of the time-weakening friction law during the nucleation process

Based on dynamic rupture simulations on a planar fault in a homogeneous half-space, we investigated the nucleation processes using the time-weakening friction law. Both the characteristic time and the rupture speed in the nucleation asperity play an important role in determining rupture behaviors on a fault plane following the time-weakening friction law, with which rupture starts from a single point in the nucleation asperity and propagates at a given speed toward the boundary of the nucleation area. Rupture with a small characteristic time or a large rupture speed in the nucleation asperity propagates earlier from the hypocenter. Rupture following the slipweakening friction law requires a smaller radius of nucleation patch to have similar rupture front contours of the time-weakening friction law. Even if the rupture velocity in the nucleation patch of the time-weakening friction law increases to infinity, the peak slip rate in the nucleation asperity is smaller than that of the slip-weakening law. The peak ground velocity distributions of ruptures following the two friction laws are also compared.

Research on TemporaI and Spatial Patterns and Dynamic Laws of Soil Water at Eco-tope between Oasis and Desert

Based on long term and stationary research, the temporal and spatial patterns and dynamic laws of soil water content in Minqin desert area were studied. Some results are as follows:(1)The change of soil water content in different years is not obviously in shrub sand dune of Nitraria sibirica and Tamarix ramosissima, but it was great in shifting sand dune, the maximum is 2.538%; (2)The season dynamics can be divided into three stages: accumulating, consuming and stable; (3) The vertical change of soil wa...

Numerical Study of Quantized Vortex Interaction in theGinzburg-Landau Equation on Bounded Domains

In this paper,we study numerically quantized vortex dynamics and their interaction in the two-dimensional(2D)Ginzburg-Landau equation(GLE)with a dimensionless parameter#>0 on bounded domains under either Dirichlet or homogeneous Neumann boundary condition.We begin with a reviewof the reduced dynamical laws for time evolution of quantized vortex centers in GLE and show how to solve these nonlinear ordinary differential equations numerically.Then we present efficient and accurate numerical methods for discretizing the GLE on either a rectangular or a disk domain under either Dirichlet or homogeneous Neumann boundary condition.Based on these efficient and accurate numerical methods for GLE and the reduced dynamical laws,we simulate quantized vortex interaction of GLE with different#and under different initial setups including single vortex,vortex pair,vortex dipole and vortex lattice,compare them with those obtained from the corresponding reduced dynamical laws,and identify the cases where the reduced dynamical laws agree qualitatively and/or quantitatively as well as fail to agree with those from GLE on vortex interaction.Finally,we also obtain numerically different patterns of the steady states for quantized vortex lattices under the GLE dynamics on bounded domains.

The application of nonlocal theory method in the coarse-grained molecular dynamics simulations of long-chain polylactic acid

The micro-capsules used for drug delivery are fabricated using polylactic acid（PLA）,which is a biomedical material approved by the FDA.A coarse-grained model of long-chain PLA was built,and molecular dynamics（MD）simulations of the model were performed using a MARTINI force field.Based on the nonlocal theory,the formula for the initial elastic modulus of polymers considering the nonlocal effect was derived,and the scaling law of internal characteristic length of polymers was proposed,which was used to adjust the cut-off radius in the MD simulations of PLA.The results show that the elastic modulus should be computed using nonlinear regression.The nonlocal effect has a certain influence on the simulation results of PLA.According to the scaling law,the cut-off radius was determined and applied to the MD simulations,the results of which reflect the influence of the molecular weight change on the elastic moduli of PLA,and are in agreement with the experimental outcome.