اشترك بالحزمة الذهبية واحصل على وصول غير محدود شمرا أكاديميا
تسجيل مستخدم جديدStochastic Dynamics of Bionanosystems: Multiscale Analysis and Specialized Ensembles
103
0
0.0
(
0
)
اسأل ChatGPT حول البحث
ﻻ يوجد ملخص باللغة العربية
An approach for simulating bionanosystems, such as viruses and ribosomes, is presented. This calibration-free approach is based on an all-atom description for bionanosystems, a universal interatomic force field, and a multiscale perspective. The supramillion-atom nature of these bionanosystems prohibits the use of a direct molecular dynamics approach for phenomena like viral structural transitions or self-assembly that develop over milliseconds or longer. A key element of these multiscale systems is the cross-talk between, and consequent strong coupling of, processes over many scales in space and time. We elucidate the role of interscale cross-talk and overcome bionanosystem simulation difficulties with automated construction of order parameters (OPs) describing supra-nanometer scale structural features, construction of OP dependent ensembles describing the statistical properties of atomistic variables that ultimately contribute to the entropies driving the dynamics of the OPs, and the derivation of a rigorous equation for the stochastic dynamics of the OPs. Since the atomic scale features of the system are treated statistically, several ensembles are constructed that reflect various experimental conditions. The theory provides a basis for a practical, quantitative bionanosystem modeling approach that preserves the cross-talk between the atomic and nanoscale features. A method for integrating information from nanotechnical experimental data in the derivation of equations of stochastic OP dynamics is also introduced.
قيم البحث
اقرأ أيضاً
We construct a path-integral representation of the generating functional for the dissipative dynamics of a classical magnetic moment as described by the stochastic generalization of the Landau-Lifshitz-Gilbert equation proposed by Brown, with the pos
sible addition of spin-torque terms. In the process of constructing this functional in the Cartesian coordinate system, we critically revisit this stochastic equation. We present it in a form that accommodates for any discretization scheme thanks to the inclusion of a drift term. The generalized equation ensures the conservation of the magnetization modulus and the approach to the Gibbs-Boltzmann equilibrium in the absence of non-potential and time-dependent forces. The drift term vanishes only if the mid-point Stratonovich prescription is used. We next reset the problem in the more natural spherical coordinate system. We show that the noise transforms non-trivially to spherical coordinates acquiring a non-vanishing mean value in this coordinate system, a fact that has been often overlooked in the literature. We next construct the generating functional formalism in this system of coordinates for any discretization prescription. The functional formalism in Cartesian or spherical coordinates should serve as a starting point to study different aspects of the out-of-equilibrium dynamics of magnets. Extensions to colored noise, micro-magnetism and disordered problems are straightforward.
Here we investigate how local properties of particles in a thermal bath influence the thermodynamics of the bath. We utilize nanothermodynamics, based on two postulates: that small systems can be treated self-consistently by coupling to an ensemble o
f similarly small systems, and that a large ensemble of small systems forms its own thermodynamic bath. We adapt these ideas to study how a large system may subdivide into an ensemble of smaller subsystems, causing internal heterogeneity across multiple size scales. For the semi-classical ideal gas, maximum entropy favors subdividing a large system of atoms into regions of variable size. The mechanism of region formation could come from quantum exchange that makes atoms in each region indistinguishable, while decoherence between regions allows atoms in separate regions to be distinguishable by location. Combining regions reduces the total entropy, as expected when distinguishable particles become indistinguishable, and as required by theorems for sub-additive entropy. Combining large volumes of small regions gives the entropy of mixing for a semi-classical ideal gas, resolving Gibbs paradox without invoking quantum symmetry for distant atoms. Other models we study are based on Ising-like spins in 1-D. We find similarity in the properties of a two-state model in the nanocanonical ensemble and a three-state model in the canonical ensemble. Thus, emergent phenomena may alter the thermal behavior of microscopic models, and the correct ensemble is necessary for fully-accurate predictions. We add a nonlinear correction to Boltzmanns factor in simulations of the Ising-like spins to imitate the dynamics of spin exchange on intermediate lengths, yielding the statistics of indistinguishable states. These simulations exhibit 1/f-like noise at low frequencies (f), and white noise at higher f, similar to the thermal fluctuations found in many materials.
We study universal aspects of fluctuations in an ensemble of noninteracting continuous quantum thermal machines in the steady state limit. Considering an individual machine, such as a refrigerator, in which relative fluctuations (and high order cumul
ants) of the cooling heat current to the absorbed heat current, $eta^{(n)}$, are upper-bounded, $eta^{(n)}leq eta_C^n$ with $ngeq 2$ and $eta_C$ the Carnot efficiency, we prove that an {it ensemble} of $N$ distinct machines similarly satisfies this upper bound on the relative fluctuations of the ensemble, $eta_N^{(n)}leq eta_C^n$. For an ensemble of distinct quantum {it refrigerators} with components operating in the tight coupling limit we further prove the existence of a {it lower bound} on $eta_N^{(n)}$ in specific cases, exemplified on three-level quantum absorption refrigerators and resonant-energy thermoelectric junctions. Beyond special cases, the existence of a lower bound on $eta_N^{(2)}$ for an ensemble of quantum refrigerators is demonstrated by numerical simulations.
We show that the fraction of time a thermodynamic current spends above its average value follows the arcsine law, a prominent result obtained by Levy for Brownian motion. Stochastic currents with long streaks above or below their average are much mor
e likely than those that spend similar fractions of time above and below their average. Our result is confirmed with experimental data from a Brownian Carnot engine. We also conjecture that two other random times associated with currents obey the arcsine law: the time a current reaches its maximum value and the last time a current crosses its average value. These results apply to, inter alia, molecular motors, quantum dots and colloidal systems.
We introduce an explicit solution for the non-equilibrium steady state (NESS) of a ring that is coupled to a thermal bath, and is driven by an external hot source with log-wide distribution of couplings. Having time scales that stretch over several d
ecades is similar to glassy systems. Consequently there is a wide range of driving intensities where the NESS is like that of a random walker in a biased Brownian landscape. We investigate the resulting statistics of the induced current $I$. For a single ring we discuss how $sign(I)$ fluctuates as the intensity of the driving is increased, while for an ensemble of rings we highlight the fingerprints of Sinai physics on the $abs(I)$ distribution.
سجل دخول لتتمكن من نشر تعليقات
التعليقات
جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
