Study of the low-temperature behavior of a disordered antiferromagnet with random fields by the parallel-tempering method

The parallel-tempering method has been applied to numerically study the thermodynamic behavior of a three-dimensional disordered antiferromagnetic Ising model with random fields at spin concentrations corresponding to regions of both weak and strong structural disorder. An analysis of the low-temperature behavior of the model convincingly shows that in the case of a weakly disordered samples there is realized an antiferromagnetic ordered state, while in the region of strong structural disorder the effects of random magnetic fields lead to the realization of a new phase state of the system with a complex domain structure consisting of antiferromagnetic and ferromagnetic domains separated by regions of a spin-glass phase and characterized by a spinglass ground state.Comment: 12 RevTeX pages, 8 figure

Diffusion and viscosity in a supercooled polydisperse system

We have carried out extensive molecular dynamics simulations of a supercooled polydisperse Lennard-Jones liquid with large variations in temperature at a fixed pressure. The particles in the system are considered to be polydisperse both in size and mass. The temperature dependence of the dynamical properties such as the viscosity ($\eta$) and the self-diffusion coefficients ($D_i$) of different size particles is studied. Both viscosity and diffusion coefficients show super-Arrhenius temperature dependence and fit well to the well-known Vogel-Fulcher-Tammann (VFT) equation. Within the temperature range investigated, the value of the Angell's fragility parameter (D $\approx 1.4$) classifies the present system into a strongly fragile liquid. The critical temperature for diffusion ($T_o^{D_i}$) increases with the size of the particles. The critical temperature for viscosity ($T_o^{\eta}$) is larger than that for the diffusion and a sizeable deviations appear for the smaller size particles implying a decoupling of translational diffusion from viscosity in deeply supercooled liquid. Indeed, the diffusion shows markedly non-Stokesian behavior at low temperatures where a highly nonlinear dependence on size is observed. An inspection of the trajectories of the particles shows that at low temperatures the motions of both the smallest and largest size particles are discontinuous (jump-type). However, the crossover from continuous Brownian to large length hopping motion takes place at shorter time scales for the smaller size particles.Comment: Revtex4, 7 pages, 8 figure

Large-Scale Atomistic Simulations of Environmental Effects on the Formation and Properties of Molecular Junctions

Using an updated simulation tool, we examine molecular junctions comprised of benzene-1,4-dithiolate bonded between gold nanotips, focusing on the importance of environmental factors and inter-electrode distance on the formation and structure of bridged molecules. We investigate the complex relationship between monolayer density and tip separation, finding that the formation of multi-molecule junctions is favored at low monolayer density, while single-molecule junctions are favored at high density. We demonstrate that tip geometry and monolayer interactions, two factors that are often neglected in simulation, affect the bonding geometry and tilt angle of bridged molecules. We further show that the structures of bridged molecules at 298 and 77 K are similar.Comment: To appear in ACS Nano, 30 pages, 5 figure

Noninvasive optical monitoring of critical closing pressure and arteriole compliance in human subjects

Sem informaçãoThe critical closing pressure (CrCP) of the cerebral circulation depends on both tissue intracranial pressure and vasomotor tone. CrCP defines the arterial blood pressure (ABP) at which cerebral blood flow approaches zero, and their difference (ABP - CrCP) is an accurate estimate of cerebral perfusion pressure. Here we demonstrate a novel noninvasive technique for continuous monitoring of CrCP at the bedside. The methodology combines optical diffuse correlation spectroscopy (DCS) measurements of pulsatile cerebral blood flow in arterioles with concurrent ABP data during the cardiac cycle. Together, the two waveforms permit calculation of CrCP via the two-compartment Windkessel model for flow in the cerebral arterioles. Measurements of CrCP by optics (DCS) and transcranial Doppler ultrasound (TCD) were carried out in 18 healthy adults; they demonstrated good agreement (R = 0.66, slope = 1.14 +/- 0.23) with means of 11.1 +/- 5.0 and 13.0 +/- 7.5 mmHg, respectively. Additionally, a potentially useful and rarely measured arteriole compliance parameter was derived from the phase difference between ABP and DCS arteriole blood flow waveforms. The measurements provide evidence that DCS signals originate predominantly from arteriole blood flow and are well suited for long-term continuous monitoring of CrCP and assessment of arteriole compliance in the clinic.37826912705Sem informaçãoSem informaçãoSem informaçãoThe author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: National Institutes of Health (grant numbers R01-NS082309-01A1, R01-NS060653, P41-EB015893, R01-NS072338, T32-HL007915), the American Heart Association (grant number 14POST20460161), and philanthropic support from the June and Steve Wolfson Family Foundation

Efficiency of adaptive temperature-based replica exchange for sampling large-scale protein conformational transitions

Temperature‐based replica exchange (RE) is now considered a principal technique for enhanced sampling of protein conformations. It is also recognized that existence of sharp cooperative transitions (such as protein folding/unfolding) can lead to temperature exchange bottlenecks and significantly reduce the sampling efficiency. Here, we revisit two adaptive temperature‐based RE protocols, namely, exchange equalization (EE) and current maximization (CM), that were previously examined using atomistic simulations (Lee and Olson, J. Chem. Physics, 134, 24111 (2011)). Both protocols aim to overcome exchange bottlenecks by adaptively adjusting the simulation temperatures, either to achieve uniform exchange rates (in EE) or to maximize temperature diffusion (CM). By designing a realistic yet computationally tractable coarse‐grained protein model, one can sample many reversible folding/unfolding transitions using conventional constant temperature molecular dynamics (MD), standard REMD, EE‐REMD, and CM‐REMD. This allows rigorous evaluation of the sampling efficiency, by directly comparing the rates of folding/unfolding transitions and convergence of various thermodynamic properties of interest. The results demonstrate that both EE and CM can indeed enhance temperature diffusion compared to standard RE, by ~3‐ and over 10‐fold, respectively. Surprisingly, the rates of reversible folding/unfolding transitions are similar in all three RE protocols. The convergence rates of several key thermodynamic properties, including the folding stability and various 1D and 2D free energy surfaces, are also similar. Therefore, the efficiency of RE protocols does not appear to be limited by temperature diffusion, but by the inherent rates of spontaneous large‐scale conformational re‐arrangements. This is particularly true considering that virtually all RE simulations of proteins in practice involve exchange attempt frequencies (~psˉ¹) that are several orders of magnitude faster than the slowest protein motions (~μsˉ¹). Our results also suggest that the efficiency of RE will not likely be improved by other protocols that aim to accelerate exchange or temperature diffusion. Instead, protocols with some types of guided tempering will likely be necessary to drive faster large‐scale conformational transitions