Optimizing Replica Exchange Moves For Molecular Dynamics

In this short note we sketch the statistical physics framework of the replica exchange technique when applied to molecular dynamics simulations. In particular, we draw attention to generalized move sets that allow a variety of optimizations as well as new applications of the method.Comment: 4 pages, 3 figures; revised version (1 figure added), PRE in pres

Diffusion in the Continuous-Imaginary-Time Quantum World-Line Monte Carlo Simulations with Extended Ensembles

The dynamics of samples in the continuous-imaginary-time quantum world-line Monte Carlo simulations with extended ensembles are investigated. In the case of a conventional flat ensemble on the one-dimensional quantum S=1 bi-quadratic model, the asymmetric behavior of Monte Carlo samples appears in the diffusion process in the space of the number of vertices. We prove that a local diffusivity is asymptotically proportional to the number of vertices, and we demonstrate the asymmetric behavior in the flat ensemble case. On the basis of the asymptotic form, we propose the weight of an optimal ensemble as $1/\sqrt{n}$, where $n$ denotes the number of vertices in a sample. It is shown that the asymmetric behavior completely vanishes in the case of the proposed ensemble on the one-dimensional quantum S=1 bi-quadratic model.Comment: 4 pages, 2 figures, update a referenc

Induction of Alloantigen-specific Anergy in Human Peripheral Blood Mononuclear Cells by Alloantigen Stimulation with Co-stimulatory Signal Blockade

Allogeneic hematopoietic stem cell transplantation (AHSCT) offers the best chance of cure for many patients with congenital and acquired hematologic diseases. Unfortunately, transplantation of alloreactive donor T cells which recognize and damage healthy patient tissues can result in Graft-versus-Host Disease (GvHD)1. One challenge to successful AHSCT is the prevention of GvHD without associated impairment of the beneficial effects of donor T cells, particularly immune reconstitution and prevention of relapse. GvHD can be prevented by non-specific depletion of donor T cells from stem cell grafts or by administration of pharmacological immunosuppression. Unfortunately these approaches increase infection and disease relapse2-4. An alternative strategy is to selectively deplete alloreactive donor T cells after allostimulation by recipient antigen presenting cells (APC) before transplant. Early clinical trials of these allodepletion strategies improved immune reconstitution after HLA-mismatched HSCT without excess GvHD5, 6. However, some allodepletion techniques require specialized recipient APC production6, 7and some approaches may have off-target effects including depletion of donor pathogen-specific T cells8and CD4 T regulatory cells9.One alternative approach is the inactivation of alloreactive donor T cells via induction of alloantigen-specific hyporesponsiveness. This is achieved by stimulating donor cells with recipient APC while providing blockade of CD28-mediated co-stimulation signals10.This "alloanergization" approach reduces alloreactivity by 1-2 logs while preserving pathogen- and tumor-associated antigen T cell responses in vitro11. The strategy has been successfully employed in 2 completed and 1 ongoing clinical pilot studies in which alloanergized donor T cells were infused during or after HLA-mismatched HSCT resulting in rapid immune reconstitution, few infections and less severe acute and chronic GvHD than historical control recipients of unmanipulated HLA-mismatched transplantation12. Here we describe our current protocol for the generation of peripheral blood mononuclear cells (PBMC) which have been alloanergized to HLA-mismatched unrelated stimulator PBMC. Alloanergization is achieved by allostimulation in the presence of monoclonal antibodies to the ligands B7.1 and B7.1 to block CD28-mediated costimulation. This technique does not require the production of specialized stimulator APC and is simple to perform, requiring only a single and relatively brief ex vivo incubation step. As such, the approach can be easily standardized for clinical use to generate donor T cells with reduced alloreactivity but retaining pathogen-specific immunity for adoptive transfer in the setting of AHSCT to improve immune reconstitution without excessive GvHD

Random Walks on a Fluctuating Lattice: A Renormalization Group Approach Applied in One Dimension

We study the problem of a random walk on a lattice in which bonds connecting nearest neighbor sites open and close randomly in time, a situation often encountered in fluctuating media. We present a simple renormalization group technique to solve for the effective diffusive behavior at long times. For one-dimensional lattices we obtain better quantitative agreement with simulation data than earlier effective medium results. Our technique works in principle in any dimension, although the amount of computation required rises with dimensionality of the lattice.Comment: PostScript file including 2 figures, total 15 pages, 8 other figures obtainable by mail from D.L. Stei

A beginner's introduction to Fukaya categories

The goal of these notes is to give a short introduction to Fukaya categories and some of their applications. The first half of the text is devoted to a brief review of Lagrangian Floer (co)homology and product structures. Then we introduce the Fukaya category (informally and without a lot of the necessary technical detail), and briefly discuss algebraic concepts such as exact triangles and generators. Finally, we mention wrapped Fukaya categories and outline a few applications to symplectic topology, mirror symmetry and low-dimensional topology. This text is based on a series of lectures given at a Summer School on Contact and Symplectic Topology at Universit\'e de Nantes in June 2011.Comment: 42 pages, 13 figure

Characterization of the stretched exponential trap-time distributions in one-dimensional coupled map lattices

Stretched exponential distributions and relaxation responses are encountered in a wide range of physical systems such as glasses, polymers and spin glasses. As found recently, this type of behavior occurs also for the distribution function of certain trap time in a number of coupled dynamical systems. We analyze a one-dimensional mathematical model of coupled chaotic oscillators which reproduces an experimental set-up of coupled diode-resonators and identify the necessary ingredients for stretched exponential distributions.Comment: 8 pages, 8 figure

A New Monte Carlo Algorithm for Protein Folding

We demonstrate that the recently proposed pruned-enriched Rosenbluth method (P. Grassberger, Phys. Rev. E 56 (1997) 3682) leads to extremely efficient algorithms for the folding of simple model proteins. We test them on several models for lattice heteropolymers, and compare to published Monte Carlo studies. In all cases our algorithms are faster than all previous ones, and in several cases we find new minimal energy states. In addition to ground states, our algorithms give estimates for the partition sum at finite temperatures.Comment: 4 pages, Latex incl. 3 eps-figs., submitted to Phys. Rev. Lett., revised version with changes in the tex

Dual function of GTPBP6 in biogenesis and recycling of human mitochondrial ribosomes

Translation and ribosome biogenesis in mitochondria require auxiliary factors that ensure rapid and accurate synthesis of mitochondrial proteins. Defects in translation are associated with oxidative phosphorylation deficiency and cause severe human diseases, but the exact roles of mitochondrial translation-associated factors are not known. Here we identify the functions of GTPBP6, a homolog of the bacterial ribosome-recycling factor HflX, in human mitochondria. Similarly to HflX, GTPBP6 facilitates the dissociation of ribosomes in vitro and in vivo. In contrast to HflX, GTPBP6 is also required for the assembly of mitochondrial ribosomes. GTPBP6 ablation leads to accumulation of late assembly intermediate(s) of the large ribosomal subunit containing ribosome biogenesis factors MTERF4, NSUN4, MALSU1 and the GTPases GTPBP5, GTPBP7 and GTPBP10. Our data show that GTPBP6 has a dual function acting in ribosome recycling and biogenesis. These findings contribute to our understanding of large ribosomal subunit assembly as well as ribosome recycling pathway in mitochondria

TRPM7 Provides an Ion Channel Mechanism for Cellular Entry of Trace Metal Ions

Trace metal ions such as Zn2+, Fe2+, Cu2+, Mn2+, and Co2+ are required cofactors for many essential cellular enzymes, yet little is known about the mechanisms through which they enter into cells. We have shown previously that the widely expressed ion channel TRPM7 (LTRPC7, ChaK1, TRP-PLIK) functions as a Ca2+- and Mg2+-permeable cation channel, whose activity is regulated by intracellular Mg2+ and Mg2+·ATP and have designated native TRPM7-mediated currents as magnesium-nucleotide–regulated metal ion currents (MagNuM). Here we report that heterologously overexpressed TRPM7 in HEK-293 cells conducts a range of essential and toxic divalent metal ions with strong preference for Zn2+ and Ni2+, which both permeate TRPM7 up to four times better than Ca2+. Similarly, native MagNuM currents are also able to support Zn2+ entry. Furthermore, TRPM7 allows other essential metals such as Mn2+ and Co2+ to permeate, and permits significant entry of nonphysiologic or toxic metals such as Cd2+, Ba2+, and Sr2+. Equimolar replacement studies substituting 10 mM Ca2+ with the respective divalent ions reveal a unique permeation profile for TRPM7 with a permeability sequence of Zn2+ ≈ Ni2+ >> Ba2+ > Co2+ > Mg2+ ≥ Mn2+ ≥ Sr2+ ≥ Cd2+ ≥ Ca2+, while trivalent ions such as La3+ and Gd3+ are not measurably permeable. With the exception of Mg2+, which exerts strong negative feedback from the intracellular side of the pore, this sequence is faithfully maintained when isotonic solutions of these divalent cations are used. Fura-2 quenching experiments with Mn2+, Co2+, or Ni2+ suggest that these can be transported by TRPM7 in the presence of physiological levels of Ca2+ and Mg2+, suggesting that TRPM7 represents a novel ion-channel mechanism for cellular metal ion entry into vertebrate cells

When the world collapses : Changed worldview and social reconstruction in a traumatized community

Background: Traumatic experience can affect the individual’s basic beliefs about the world as a predictable and safe place. One of the cornerstones in recovery from trauma is reestablishment of safety, connectedness, and the shattered schema of a worldview. Objective: This study explored the role of negatively changed worldview in the relationship between war-related traumatization and readiness for social reconstruction of intergroup relations in a post-conflict community measured by three processes: intergroup rapprochement, rebuilding trust, and need for apology. It was hypothesized that more traumatized people are less supportive of social reconstruction and that this relationship is mediated by the changed worldview. Method: The study included a community random sample of 333 adults in the city of Vukovar, Croatia, that was most devastated during the 1991–1995 war. Six instruments were administered: Stressful Events Scale, Impact of Event Scale-Revised, Changed Worldview Scale, and three scales measuring the post-conflict social reconstruction processes: Intergroup Rapprochement, Intergroup Trust and Need for Apology. Results: Mediation analyses showed that the worldview change fully mediated between traumatization and all three aspects of social reconstruction. Conclusions: In a population exposed to war traumatization the worldview change mediates post-conflict social recovery of community relations