Temperature control in molecular dynamic simulations of non-equilibrium processes

Thermostats are often used in various condensed matter problems, e.g. when a biological molecule undergoes a transformation in a solution, a crystal surface is irradiated with energetic particles, a crack propagates in a solid upon applied stress, two surfaces slide with respect to each other, an excited local phonon dissipates its energy into a crystal bulk, and so on. In all of these problems, as well as in many others, there is an energy transfer between different local parts of the entire system kept at a constant temperature. Very often, when modelling such processes using molecular dynamics simulations, thermostatting is done using strictly equilibrium approaches serving to describe the NV T ensemble. In this paper we critically discuss the applicability of such approaches to non-equilibrium problems, including those mentioned above, and stress that the correct temperature control can only be achieved if the method is based on the generalized Langevin equation (GLE). Specifically, we emphasize that a meaningful compromise between computational efficiency and a physically appropriate implementation of the NV T thermostat can be achieved, at least for solid state and surface problems, if the so-called stochastic boundary conditions (SBC), recently derived from the GLE (Kantorovich and Rompotis 2008 Phys. Rev. B 78 094305), are used. For SBC, the Langevin thermostat is only applied to the outer part of the simulated fragment of the entire system which borders the surrounding environment (not considered explicitly) serving as a heat bath. This point is illustrated by comparing the performance of the SBC and some of the equilibrium thermostats in two problems: (i) irradiation of the Si(001) surface with an energetic CaF2 molecule using an ab initio density functional theory based method, and (ii) the tribology of two amorphous SiO2 surfaces coated with self-assembled monolayers of methyl-terminated hydrocarbon alkoxylsilane molecules using a classical atomistic force field. We discuss the differences in behaviour of these systems due to applied thermostatting, and show that in some cases a qualitatively different physical behaviour of the simulated system can be obtained if an equilibrium thermostat is used

Protein kinase C and cardiac dysfunction: a review

Heart failure (HF) is a physiological state in which cardiac output is insufficient to meet the needs of the body. It is a clinical syndrome characterized by impaired ability of the left ventricle to either fill or eject blood efficiently. HF is a disease of multiple aetiologies leading to progressive cardiac dysfunction and it is the leading cause of deaths in both developed and developing countries. HF is responsible for about 73,000 deaths in the UK each year. In the USA, HF affects 5.8 million people and 550,000 new cases are diagnosed annually. Cardiac remodelling (CD), which plays an important role in pathogenesis of HF, is viewed as stress response to an index event such as myocardial ischaemia or imposition of mechanical load leading to a series of structural and functional changes in the viable myocardium. Protein kinase C (PKC) isozymes are a family of serine/threonine kinases. PKC is a central enzyme in the regulation of growth, hypertrophy, and mediators of signal transduction pathways. In response to circulating hormones, activation of PKC triggers a multitude of intracellular events influencing multiple physiological processes in the heart, including heart rate, contraction, and relaxation. Recent research implicates PKC activation in the pathophysiology of a number of cardiovascular disease states. Few reports are available that examine PKC in normal and diseased human hearts. This review describes the structure, functions, and distribution of PKCs in the healthy and diseased heart with emphasis on the human heart and, also importantly, their regulation in heart failure

Microstructure and hardness characterisation of laser coatings produced with a mixture of AISI 420 stainless steel and Fe-C-Cr-Nb-B-Mo steel alloy powders

Fe-C-Cr-Nb-B-Mo alloy powder and AISI 420 SS powder are deposited using laser cladding to increase the hardness for wear resistant applications. Mixtures from 0 to 100 wt.% were evaluated to understand the effect on the elemental composition, microstructure, phases, and microhardness. The mixture of carbon, boron and niobium in the Fe-C-Cr-Nb-B-Mo alloy powder introduces complex carbides into a Fe-based matrix of AISI 420 SS which increases its hardness. Hardness increased linearly with increasing Fe-C-Cr-Nb-B-Mo alloy, but substantial micro-cracking was observed in the clad layer at additions of 60 wt.% and above; related to a transition from a hypoeutectic alloy containing α-Fe/α' dendrites with an (Fe,Cr)2B and γ-Fe eutectic to primary and continuous carbo-borides M2B (where M represents Fe and Cr) and M23(B,C)6 carbides (where M represents Fe, Cr, Mo) with MC particles (where M represents Nb and Mo). The highest average hardness, for an alloy without micro-cracking, of 952 HV was observed in a 40 wt.% alloy. High stress abrasive scratch testing was conducted on all alloys at various loads (500, 1500, 2500 N). Alloy content was found to have a strong effect on the wear mode and the abrasive wear rate, and the presence of micro-cracks was detrimental to abrasive wear resistance

Structure of the indium-rich InSb(001) surface

The indium-rich InSb(001) surface, that shows the c(8×2) reconstruction at room temperature and a partially disordered phase at 77 K (the low temperature or LT phase), is studied experimentally by means of scanning probe microscopies, low-energy electron diffraction, and angle-resolved photoelectron spectroscopy (ARPES), as well as theoretically, using the density-functional theory (DFT). The experimental studies are done both at room temperature and at cryogenic temperatures. No metallic surface bands are found using ARPES, consequently the idea of charge-density waves as a possible explanation of the LT phase suggested previously by Goryl et al. [Surf. Sci. 601, 3605 (2007)] is discarded. On the other hand it is shown that an essential core of the surface structure is described by the so-called ζ model which has the c(8×2) symmetry. However, on top of this basic structure there are additional not fully occupied indium-atom rows. Vacancies/atoms in these rows rapidly fluctuate at room temperature while, upon cooling down, they stabilize to form a sublattice also of c(8×2) symmetry. Furthermore, this sublattice has shifted mirror symmetry axes (relating to those of the underlying ζ lattice) therefore the surface symmetry is lowered from c2mm to p2 and structural domains are formed. This occurs with no significant core ζ lattice distortions but dense domain borders lead to significant disorder in the top atomic layer. DFT calculations confirm that the postulated ζ-like structure with additional 50% occupied indium-atom rows is stable on the InSb (001) surface. Calculated, in the Tersoff-Hammann approximation, scanning tunneling microscopy (STM) images of the relaxed surface structure agree well with experimental STM images