Survival of Virus Particles in Water Droplets: Hydrophobic Forces and Landauer’s Principle

Many small biological objects, such as viruses, survive in a water environment and cannot remain active in dry air without condensation of water vapor. From a physical point of view, these objects belong to the mesoscale, where small thermal fluctuations with the characteristic kinetic energy of k_BT (where k_B is the Boltzmann’s constant and T is the absolute temperature) play a significant role. The self-assembly of viruses, including protein folding and the formation of a protein capsid and lipid bilayer membrane, is controlled by hydrophobic forces (i.e., the repulsing forces between hydrophobic particles and regions of molecules) in a water environment. Hydrophobic forces are entropic, and they are driven by a system’s tendency to attain the maximum disordered state. On the other hand, in information systems, entropic forces are responsible for erasing information, if the energy barrier between two states of a switch is on the order of k_BT, which is referred to as Landauer’s principle. We treated hydrophobic interactions responsible for the self-assembly of viruses as an information-processing mechanism. We further showed a similarity of these submicron-scale processes with the self-assembly in colloidal crystals, droplet clusters, and liquid marbles.     

Thermodynamic properties of water in confined environments: a Monte Carlo study

Monte Carlo simulations of Mercedes-Benz water in a crowded environment were performed. The simulated systems are representative of both composite, porous or sintered materials and living cells with typical matrix packings. We studied the influence of overall temperature as well as the density and size of matrix particles on water density, particle distributions, hydrogen bond formation and thermodynamic quantities. Interestingly, temperature and space occupancy of matrix exhibit a similar effect on water properties following the competition between the kinetic and the potential energy of the system, whereby temperature increases the kinetic and matrix packing decreases the potential contribution. A novel thermodynamic decomposition approach was applied to gain insight into individual contributions of different types of inter-particle interactions. This decomposition proved to be useful and in good agreement with the total thermodynamic quantities especially at higher temperatures and matrix packings, where higher-order potential-energy mixing terms lose their importance.     

Econophysics and the Entropic Foundations of Economics

This paper examines relations between econophysics and the law of entropy as foundations of economic phenomena. Ontological entropy, where actual thermodynamic processes are involved in the flow of energy from the Sun through the biosphere and economy, is distinguished from metaphorical entropy, where similar mathematics used for modeling entropy is employed to model economic phenomena. Areas considered include general equilibrium theory, growth theory, business cycles, ecological economics, urban–regional economics, income and wealth distribution, and financial market dynamics. The power-law distributions studied by econophysicists can reflect anti-entropic forces is emphasized to show how entropic and anti-entropic forces can interact to drive economic dynamics, such as in the interaction between business cycles, financial markets, and income distributions.     

Three-dimensional binary superlattices of oppositely charged colloids

We report the equilibrium self-assembly of binary crystals of oppositely charged colloidal microspheres at high density. By varying the magnitude of the charge on near equal-sized spheres we show that the structure of the binary crystal may be switched between face-centered cubic, cesium chloride, and sodium chloride. We interpret these transformations in terms of a competition between entropic and Coulombic forces.     

Dynamics of Ion Channels via Non-Hermitian Quantum Mechanics

We study dynamics and thermodynamics of ion transport in narrow, water-filled channels, considered as effective 1D Coulomb systems. The long range nature of the inter-ion interactions comes about due to the dielectric constants mismatch between the water and the surrounding medium, confining the electric filed to stay mostly within the water-filled channel. Statistical mechanics of such Coulomb systems is dominated by entropic effects which may be accurately accounted for by mapping onto an effective quantum mechanics. In presence of multivalent ions the corresponding quantum mechanics appears to be non-Hermitian. In this review we discuss a framework for semiclassical calculations for the effective non-Hermitian Hamiltonians. Non-Hermiticity elevates WKB action integrals from the real line to closed cycles on a complex Riemann surfaces where direct calculations are not attainable. We circumvent this issue by applying tools from algebraic topology, such as the Picard-Fuchs equation. We discuss how its solutions relate to the thermodynamics and correlation functions of multivalent solutions within narrow, water-filled channels.     

Poly-dimethylsiloxane derivates side chains effect on syntan functionalized Polyamide fabric

Poly-dimethylsiloxane (PDMS) polymers finishing of Polyamide-6,6 (PA66) fabrics involves ionic interactions between reactive groups on the PDMS polymers and the ones of the textile fabric. Such interactions could be strengthened by a pretreatment with a fixing agent to promote either ion-ion and H-bonding and ion-dipole forces. These forces could contribute towards the building of substantial PDMS-PA66 systems and the achieving of better adhesion properties to fabrics. Four different silicone polymers based on PDMS were applied on a synthetic tanning agent (syntan) finished Polyamide-6,6 fabric under acid conditions. Soxhlet extraction method and ATR FT-IR technique were used to investigate the application conditions. The finishing parameters such as pH and temperature together with fastness, mechanical and performance properties of the treated samples were studied and related to PDMS side chains effect on syntan functionalized Polyamide fabric.     

自驱动颗粒体系中的熵力

在许多纳米复合材料体系中熵力(entropy force)是普遍存在的,但由于熵力的存在会导致纳米颗粒的凝聚从而降低其许多性能,因此在大多数情况下熵力的存在对体系并无益处,所以研究如何减小熵力对体系的影响是非常重要的.不带角速度的自驱动粒子在熵力作用下会集聚在纳米颗粒(或者纳米棒)周围,这会对纳米颗粒(或者纳米棒)产生很大的相互作用力.对于纳米颗粒,在不带角速度的自驱动粒子体系中存在着非常大的排斥力.而对于纳米棒,由于纳米棒内外的不对称性,使得两个纳米棒之间会产生吸引-排斥转变,同时这个吸引-排斥转变与纳米棒之间的距离有关.当自驱动粒子加上一个自转角速度ω之后,熵力的作用就大大减弱,纳米颗粒不再集聚.研究结果有助于对非平衡态下纳米颗粒(或纳米棒)之间熵相互作用力的认识.     

Entropic Uncertainty in Neutrino and Meson Systems

The dynamics of quantum‐memory‐assisted entropic uncertainty for the closed neutrino system in the context of two flavor oscillations and the meson system within the framework of open quantum system are investigated. It is found that the entropic uncertainty exists in close relation with the quantum correlation, and growing quantum correlation can decrease the uncertainty. The oscillatory behaviors of entropic uncertainty in neutrino system brought about by neutrino oscillating property are different from the decaying behaviors of entropic uncertainty in meson system induced by the meson decaying nature. In addition, the entropic uncertainty is always equal to its lower bound in the two subatomic systems. This study would throw light on the particle behavior characteristics of high energy physics, and may be useful to the tasks of quantum information‐processing implemented with subatomic system since the uncertainty principle plays vital role in quantum information science and technology.     

Effect of Quantum Coherence on Landauer’s Principle

Landauer’s principle provides a fundamental lower bound for energy dissipation occurring with information erasure in the quantum regime. While most studies have related the entropy reduction incorporated with the erasure to the lower bound (entropic bound), recent efforts have also provided another lower bound associated with the thermal fluctuation of the dissipated energy (thermodynamic bound). The coexistence of the two bounds has stimulated comparative studies of their properties; however, these studies were performed for systems where the time-evolution of diagonal (population) and off-diagonal (coherence) elements of the density matrix are decoupled. In this paper, we aimed to broaden the comparative study to include the influence of quantum coherence induced by the tilted system–reservoir interaction direction. By examining their dependence on the initial state of the information-bearing system, we find that the following properties of the bounds are generically held regardless of whether the influence of the coherence is present or not: the entropic bound serves as the tighter bound for a sufficiently mixed initial state, while the thermodynamic bound is tighter when the purity of the initial state is sufficiently high. The exception is the case where the system dynamics involve only phase relaxation; in this case, the two bounds coincide when the initial coherence is zero; otherwise, the thermodynamic bound serves the tighter bound. We also find the quantum information erasure inevitably accompanies constant energy dissipation caused by the creation of system–reservoir correlation, which may cause an additional source of energetic cost for the erasure.     

A phenomenological explanation for the buckling of surface alloys

A phenomenological model, in which the interactions between the nearest-neighbor (NN) atoms are described as bondings but not hard sphere contacts, is proposed to explain the unexpected reduced buckling in surface alloy systems. In the model, the forces acting on an adsorbate atom from its NN substrate atoms in different layers may be either repulsive or attractive, depending on whether the bond between the adsorbate atom and its NN substrate atoms is compressed or stretched. It is found that the forces on the adsorbate atom from its NN substrate atoms in the sub-surface layer play a more important role for the buckling of surface alloy than those from its NN substrate atoms in the surface layer do. The bucklings expected by the model are significantly smaller than those predicted by the simple hard sphere model and are in good agreement with the experiments when the equilibrium bond length of the NN adsorbate-substrate atom pairs is taken as the sum of the corresponding metal radii.     

活细胞中的化学物理-光学观测和控制细胞内信号转导

Cells are crowded microenvironments filled with macromolecules undergoing constant physical and chemical interactions. The physicochemical makeup of the cells affects various cellular responses, determines cell-cell interactions and influences cell decisions. Chemical and physical properties differ between cells and within cells. Moreover, these properties are subject to dynamic changes in response to environmental signals, which often demand adjustments in the chemical or physical states of intracellular molecules. Indeed, cellular responses such as gene expression rely on the faithful relay of information from the outside to the inside of the cell, a process termed signal transduction. The signal often traverses a complex path across subcellular spaces with variable physical chemistry, sometimes even influencing it. Understanding the molecular states of such signaling molecules and their intracellular environments is vital to our understanding of the cell. Exploring such intricate spaces is possible today largely because of experimental and theoretical tools. Here, we focus on one tool that is commonly used in chemical physics studies-light. We summarize recent work which uses light to both visualize the cellular environment and also control intracellular processes along the axis of signal transduction. We highlight recent accomplishments in optical microscopy and optogenetics, an emerging experimental strategy which utilizes light to control the molecular processes in live cells. We believe that optogenetics lends unprecedented spatiotemporal precision to the manipulation of physicochemical properties in biological contexts. We hope to use this work to demonstrate new opportunities for chemical physicists who are interested in pursuing biological and biomedical questions.     

Entropy Method of Road Safety Management: Case Study of the Russian Federation

Within the framework of this paper, the author’s entropy method of road safety management in large-sized systems is considered. The road safety management system in the Russian Federation, the largest country in the world, was selected for this case study. The purpose of the article is to present the opportunities and methodology of the use of quantitative assessments of the orderliness of the road accident rate formation process in regional transport systems for road safety management. Orderliness, in other words, systemic anti-chaos, can be quantified using the C. Shannon informational entropy H. The article consists of the results of the issue’s state analysis; methodology of assessment of the orderliness of the road accident rate formation process based on the using of the cause-and-effect chain; entropic method of the road safety management in large-scale systems, in particular, the algorithm of management of regional road safety in Russia taking into account the level of its entropic orderliness; and examples of the quantitative evaluation of the orderliness of regional road safety provision systems in Russia. The key results of the research are spatio-temporal patterns of the change of the orderliness of the road safety provision systems in the Russian Federation in 2004–2020. Based on the results, conclusions and recommendations about the practical application of the entropic method of road safety management in large federal states with complex administrative structures were formulated. These results give an idea of the possibilities of the usage of entropic approaches in road safety management to assess the orderliness of the regional transport systems and the advantages of the entropic method over other managerial methods.     

Theory of microphase separation on side-chain liquid-crystalline polymers with flexible spacers

We model a melt of monodisperse side-chain liquid-crystalline polymers as a melt of comb copolymers in which the side groups are rod-coil diblock copolymers. We consider both excluded-volume and Maier-Saupe interactions. The first acts among any pair of segments while the latter acts only between rods. Using a free-energy functional calculated from this microscopic model, we study the spinodal stability of the isotropic phase against density and orientational fluctuations. The phase diagram obtained in this way predicts nematic and smectic instabilities as well as the existence of microphases or phases with modulated wave vector but without nematic ordering. Such microphases are the result of the competition between the incompatibility among the blocks and the connectivity constraints imposed by the spacer and the backbone. Also the effects of the polymerization degree and structural conformation of the monomeric units on the phase behavior of the side-chain liquid-crystalline polymers are studied.     

Relativity,thermodynamics and entropic forces

A recent assertion that inertial and gravitational forces are entropic forces is discussed. A more conventional approach is stressed herein, whereby entropy is treated as a result of relative motion between observers in different frames of reference. It is demonstrated that the entropy associated with inertial and gravitational forces is dependent upon the well known lapse function of general relativity. An interpretation of the temperature and entropy of an accelerating body is then developed, and used to relate the entropic force to Newton's second law of motion. The entropic force is also derived in general coordinates. An expression of the gravitational entropy of in‐falling matter is then derived by way of Schwarzschild coordinates. As a final consideration, the entropy of a weakly gravitating matter distribution is shown to be proportional to the self‐energy and the stress‐energy‐momentum content of the matter distribution.     

Operator Correlations and Quantum Regression Theorem in Non-Markovian Lindblad Rate Equations

Non-Markovian Lindblad rate equations arise from alternative microscopic interactions such as quantum systems coupled to composite reservoirs, where extra degrees of freedom mediate the interaction between the system and a Markovian reservoir, as well as from systems coupled to complex structured reservoirs whose action can be well approximated by a direct sum of Markovian sub-reservoirs (Budini in Phys. Rev. A 74:053815 [2006]). The purpose of this paper is two fold. First, for both kinds of interactions we find general expressions for the system operator correlations written in terms of the Lindblad rate propagator. Secondly, we find the conditions under which a quantum regression hypothesis is valid. We show that a non-Markovian quantum regression theorem can only be granted in a stationary regime, being a necessary condition the fulfillment of a detailed balance condition. This result is independent of the underlying microscopic interaction, providing a criterion for the validity of the regression hypothesis in non-Markovian Lindblad-like master equations. As an example, we study the correlations of a two-level system coupled to different kind of reservoirs.     

Theory of thermally activated ionization and dissociation of bound states

Calculating the microscopic dissociation rate of a bound state, such as a classical diatomic molecule, has been difficult so far. The problem was that standard theories require an energy barrier over which the bound particle (or state) escapes into the preferred low-energy state. This is not the case when the long-range repulsion responsible for the barrier is either absent or screened (as in Cooper pairs, plasmas, or biomolecular complexes). We solve this classical problem by accounting for entropic driving forces at the microscopic level. The theory predicts dissociation rates for arbitrary potentials and is successfully tested on the example of plasma, where it yields an estimate of ionization in the core of the Sun in excellent agreement with experiments. In biology, the new theory accounts for crowding in receptor-ligand kinetics and protein aggregation.     

New approaches in agent-based modeling of complex financial systems

Agent-based modeling is a powerful simulation technique to understand the collective behavior and microscopic interaction in complex financial systems. Recently, the concept for determining the key parameters of agent-based models from empirical data instead of setting them artificially was suggested. We first review several agent-based models and the new approaches to determine the key model parameters from historical market data. Based on the agents’ behaviors with heterogeneous personal preferences and interactions, these models are successful in explaining the microscopic origination of the temporal and spatial correlations of financial markets. We then present a novel paradigm combining big-data analysis with agent-based modeling. Specifically, from internet query and stock market data, we extract the information driving forces and develop an agent-based model to simulate the dynamic behaviors of complex financial systems.     

Depletion effects and loop formation in self-avoiding polymers

Langevin dynamics is employed to study the looping kinetics of self-avoiding polymers both in ideal and crowded solutions. A rich kinetics results from the competition of two crowding-induced effects: the depletion attraction and the enhanced viscous friction. For short chains, the enhanced friction slows down looping, while for longer chains, the depletion attraction renders it more frequent and persistent. We discuss the possible relevance of the findings for chromatin looping in living cells.