Juan P. Garrahan

Bio: Juan P. Garrahan is an academic researcher from University of Nottingham. The author has contributed to research in topics: Phase transition & Quantum. The author has an hindex of 55, co-authored 260 publications receiving 10600 citations. Previous affiliations of Juan P. Garrahan include University of Buenos Aires & University of Bath.

Dynamics on the Way to Forming Glass: Bubbles in Space-Time

Abstract: We review a theoretical perspective of the dynamics of glass-forming liquids and the glass transition, a perspective developed during this past decade based on the structure of trajectory space. This structure emerges from spatial correlations of dynamics that appear in disordered systems as they approach nonergodic or jammed states. It is characterized in terms of dynamical heterogeneity, facilitation, and excitation lines. These features are associated with a newly discovered class of nonequilibrium phase transitions. Equilibrium properties have little, if anything, to do with it. The broken symmetries of these transitions are obscure or absent in spatial structures, but they are vivid in space-time (i.e., trajectory space). In our view, the glass transition is an example of this class of transitions. The basic ideas and principles we review were originally developed through the analysis of idealized and abstract models. Nevertheless, the central ideas are easily illustrated with reference to molecular dynamics of more realistic atomistic models, and we use that illustrative approach here.

Dynamical first-order phase transition in kinetically constrained models of glasses.

Abstract: We show that the dynamics of kinetically constrained models of glass formers takes place at a first-order coexistence line between active and inactive dynamical phases. We prove this by computing the large-deviation functions of suitable space-time observables, such as the number of configuration changes in a trajectory. We present analytic results for dynamic facilitated models in a mean-field approximation, and numerical results for the Fredrickson-Andersen model, the East model, and constrained lattice gases, in various dimensions. This dynamical first-order transition is generic in kinetically constrained models, and we expect it to be present in systems with fully jammed states.

Dynamic Order-Disorder in Atomistic Models of Structural Glass Formers

Abstract: The glass transition is the freezing of a liquid into a solid state without evident structural order. Although glassy materials are well characterized experimentally, the existence of a phase transition into the glass state remains controversial. Here, we present numerical evidence for the existence of a novel first-order dynamical phase transition in atomistic models of structural glass formers. In contrast to equilibrium phase transitions, which occur in configuration space, this transition occurs in trajectory space, and it is controlled by variables that drive the system out of equilibrium. Coexistence is established between an ergodic phase with finite relaxation time and a nonergodic phase of immobile molecular configurations. Thus, we connect the glass transition to a true phase transition, offering the possibility of a unified picture of glassy phenomena.

Geometrical explanation and scaling of dynamical heterogeneities in glass forming systems.

Abstract: We show how dynamical heterogeneities in glass forming systems emerge as a consequence of the existence of dynamical constraints, and we offer an interpretation of the glass transition as an entropy crisis in trajectory space (space-time) rather than in configuration space. To illustrate our general ideas, we analyze the one-dimensional d 1 Fredrickson-Andersen and East models. Dynamics of such dynamically constrained systems are shown to be isomorphic to the statics of (d 1 1)-dimensional dense mixtures of polydisperse noninterpenetrating domains. The domains coincide with arrested regions in trajectory space.

First-order dynamical phase transition in models of glasses: an approach based on ensembles of histories

Abstract: We investigate the dynamics of kinetically constrained models of glass formers by analysing the statistics of trajectories of the dynamics, or histories, using large deviation function methods. We show that, in general, these models exhibit a first-order dynamical transition between active and inactive dynamical phases. We argue that the dynamical heterogeneities displayed by these systems are a manifestation of dynamical first-order phase coexistence. In particular, we calculate dynamical large deviation functions, both analytically and numerically, for the Fredrickson–Andersen model, the East model, and constrained lattice gas models. We also show how large deviation functions can be obtained from a Landau-like theory for dynamical fluctuations. We discuss possibilities for similar dynamical phase-coexistence behaviour in other systems with heterogeneous dynamics.

I and i

Abstract: There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality. Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

Phd by thesis

Abstract: Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Stochastic Processes in Physics and Chemistry

Abstract: N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.