Modeling Brownian Motion as a Timelapse of the Physical, Persistent Trajectory

被引:0
作者
Cademartiri, Ludovico [1 ]
机构
[1] Univ Parma, Dept Chem Life Sci & Environm Sustainabil, I-43121 Parma, Italy
关键词
MOLECULAR-DYNAMICS; SHEAR-FLOW; LIQUIDS; VISCOSITY;
D O I
10.1021/acs.jpcb.4c07685
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
While it is very common to model diffusion as a random walk by assuming memorylessness of the trajectory and diffusive step lengths, these assumptions can lead to significant errors. This paper describes the extent to which the physical trajectory of a Brownian particle can be described by a random walk. Analysis of "timelapses" of physical trajectories (calculated over collisional time scales using a velocity autocorrelation function that captures the hydrodynamic and acoustic effects induced by the solvent) yielded two observations: (i) these subsampled trajectories become genuinely memoryless only when their time step is similar to 200 times larger than the relaxation time, and (ii) the distributions of the subsampled step lengths have variances that are significantly smaller than the diffusional ones (usually by a factor of similar to 2). This last observation is due to two facts: diffusional displacements are mathematically "superballistic" at short time scales, and subsampled trajectories are "moving averages" of the underlying physical trajectory. The counterintuitive result is that the mean squared displacement (MSD) of the physical trajectory asymptotically approaches 2Dt (where D is diffusivity) at long time intervals t, but the MSD of the individual subsampled steps does not, even when their duration is several hundred times larger than the relaxation time. I discuss how to best account for this effect in computational approaches.
引用
收藏
页码:5511 / 5519
页数:9
相关论文
共 38 条
[11]   BROWNIAN MOTION OF A SPHERICAL-PARTICLE IN A COMPRESSIBLE FLUID [J].
CHOW, TS ;
HERMANS, JJ .
PHYSICA, 1973, 65 (01) :156-162
[12]   BROWNIAN PARTICLES IN SHEAR-FLOW AND HARMONIC POTENTIALS - A STUDY OF LONG-TIME TAILS [J].
CLERCX, HJH ;
SCHRAM, PPJM .
PHYSICAL REVIEW A, 1992, 46 (04) :1942-1950
[13]   THE NUMERICAL STABILITY OF THE LEVINSON-DURBIN ALGORITHM FOR TOEPLITZ-SYSTEMS OF EQUATIONS [J].
CYBENKO, G .
SIAM JOURNAL ON SCIENTIFIC AND STATISTICAL COMPUTING, 1980, 1 (03) :303-319
[14]   Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems [J].
Gkeka, Paraskevi ;
Stoltz, Gabriel ;
Farimani, Amir Barati ;
Belkacemi, Zineb ;
Ceriotti, Michele ;
Chodera, John D. ;
Dinner, Aaron R. ;
Ferguson, Andrew L. ;
Maillet, Jean-Bernard ;
Minoux, Herve ;
Peter, Christine ;
Pietrucci, Fabio ;
Silveira, Ana ;
Tkatchenko, Alexandre ;
Trstanova, Zofia ;
Wiewiora, Rafal ;
Lelievre, Tony .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2020, 16 (08) :4757-4775
[15]   The ugly, bad, and good stories of large-scale biomolecular simulations [J].
Gupta, Chitrak ;
Sarkar, Daipayan ;
Tieleman, D. Peter ;
Singharoy, Abhishek .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 2022, 73
[16]   NEW CORRELATION FOR SATURATED DENSITIES OF LIQUIDS AND THEIR MIXTURES [J].
HANKINSON, RW ;
THOMSON, GH .
AICHE JOURNAL, 1979, 25 (04) :653-663
[17]   APPLICATION OF LANGEVIN EQUATION TO FLUID SUSPENSIONS [J].
HINCH, EJ .
JOURNAL OF FLUID MECHANICS, 1975, 72 (DEC9) :499-511
[18]  
Huang R., 2008, BROWNIAN MOTION FAST
[19]   Brownian Dynamics Simulations of Biological Molecules [J].
Huber, Gary A. ;
McCammon, J. Andrew .
TRENDS IN CHEMISTRY, 2019, 1 (08) :727-738
[20]   Diffusing diffusivity: Rotational diffusion in two and three dimensions [J].
Jain, Rohit ;
Sebastian, K. L. .
JOURNAL OF CHEMICAL PHYSICS, 2017, 146 (21)