Michal Borkovec

Bio: Michal Borkovec is an academic researcher from University of Geneva. The author has contributed to research in topics: Polyelectrolyte & DLVO theory. The author has an hindex of 66, co-authored 235 publications receiving 19638 citations. Previous affiliations of Michal Borkovec include Max Planck Society & Clarkson University.

Reaction-rate theory: fifty years after Kramers

Abstract: The calculation of rate coefficients is a discipline of nonlinear science of importance to much of physics, chemistry, engineering, and biology. Fifty years after Kramers' seminal paper on thermally activated barrier crossing, the authors report, extend, and interpret much of our current understanding relating to theories of noise-activated escape, for which many of the notable contributions are originating from the communities both of physics and of physical chemistry. Theoretical as well as numerical approaches are discussed for single- and many-dimensional metastable systems (including fields) in gases and condensed phases. The role of many-dimensional transition-state theory is contrasted with Kramers' reaction-rate theory for moderate-to-strong friction; the authors emphasize the physical situation and the close connection between unimolecular rate theory and Kramers' work for weakly damped systems. The rate theory accounting for memory friction is presented, together with a unifying theoretical approach which covers the whole regime of weak-to-moderate-to-strong friction on the same basis (turnover theory). The peculiarities of noise-activated escape in a variety of physically different metastable potential configurations is elucidated in terms of the mean-first-passage-time technique. Moreover, the role and the complexity of escape in driven systems exhibiting possibly multiple, metastable stationary nonequilibrium states is identified. At lower temperatures, quantum tunneling effects start to dominate the rate mechanism. The early quantum approaches as well as the latest quantum versions of Kramers' theory are discussed, thereby providing a description of dissipative escape events at all temperatures. In addition, an attempt is made to discuss prominent experimental work as it relates to Kramers' reaction-rate theory and to indicate the most important areas for future research in theory and experiment.

Mobile Subsurface Colloids and Their Role in Contaminant Transport

Abstract: Publisher Summary It is noted that colloidal particles can be effectively transported through subsurface porous media under certain hydrogeochemical conditions. If present in large concentrations, mobile colloids can act as carriers for strongly sorbing contaminants and thereby provide an unretarded transport pathway for contaminants that are otherwise strongly retarded. This potential transport pathway can be considered in risk assessments of sites heavily contaminated with toxic chemicals, such as certain radionuclides, heavy metals, and hydrophobic organic compounds. The chapter reviews the current state of knowledge about the behavior of colloids in porous media and their role in contaminant transport. The chapter also identifies some important future research needs. Colloids are commonly defined as small particles or other entities with dimensions roughly between 1 nm and 1 μm. These size limits to dissolved molecules on one side and to larger suspended particles on the other side. Colloidal particles remain stable in suspension over long time periods, unless they coagulate to form larger aggregates or deposit onto surfaces of larger grains.

Coagulation Rate Measurements of Colloidal Particles by Simultaneous Static and Dynamic Light Scattering

Abstract: In this work we study the kinetics of coagulation of monodisperse spherical colloids in aqueous suspension at the early stage of coagulation. We have performed the measurements on a multiangle static and dynamic light scattering instrument using a fiber-optics-based detection system which permits simultaneous time-resolved measurements at different angles. The absolute coagulation rate constants are determined from the change of the scattering light intensity as well as from the increase of the hydrodynamic radius at different angles. The combined evaluation of static and dynamic light scattering results permits the determination of coagulation rate constants without the explicit use of light scattering form factors for the aggregates. For different electrolytes fast coagulation rate constants were estimated. Stability curves were measured as a function of ionic strength using different particle concentrations.

Aggregation and charging of colloidal silica particles: effect of particle size.

Abstract: We studied systematically aqueous suspensions of amorphous well-characterized silica particles by potentiometric titration, electrophoretic mobility, and time-resolved light scattering. Their charging behavior and aggregation rate constants were measured as a function of pH and ionic strength in KCl electrolytes for three types of particles of approximately 30, 50, and 80 nm in diameter. The charging behavior was consistent with the basic Stern model; the silica particles carry a negative charge, and its magnitude gradually increases with increasing pH and ionic strength. On the other hand, their early-stage aggregation (or coagulation) behavior is complex. The aggregation of the largest particles shows features resembling predictions of the Derjaguin, Landau, Verwey, and Overbeek (DLVO) theory. On one hand, the rate constant decreases sharply with increasing pH at low ionic strengths and attains fast aggregation conditions at high ionic strengths. On the other hand, we observe a characteristic slowing down of the aggregation at low pH and high ionic strengths. This feature becomes very pronounced for the medium and the small particles, leading to a complete stabilization at low pH for the latter. Stabilization is also observed at higher pH for the medium and the small particles. From these aggregation measurements we infer the existence of an additional repulsive force. Its origin is tentatively explained by postulating hairy layers of consisting of poly(silicilic acid) chains on the particle surface.

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。

CHARMM: the biomolecular simulation program.

Abstract: CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.

Magnetic Iron Oxide Nanoparticles: Synthesis, Stabilization, Vectorization, Physicochemical Characterizations, and Biological Applications

Abstract: 1. Introduction 20642. Synthesis of Magnetic Nanoparticles 20662.1. Classical Synthesis by Coprecipitation 20662.2. Reactions in Constrained Environments 20682.3. Hydrothermal and High-TemperatureReactions20692.4. Sol-Gel Reactions 20702.5. Polyol Methods 20712.6. Flow Injection Syntheses 20712.7. Electrochemical Methods 20712.8. Aerosol/Vapor Methods 20712.9. Sonolysis 20723. Stabilization of Magnetic Particles 20723.1. Monomeric Stabilizers 20723.1.1. Carboxylates 20733.1.2. Phosphates 20733.2. Inorganic Materials 20733.2.1. Silica 20733.2.2. Gold 20743.3. Polymer Stabilizers 20743.3.1. Dextran 20743.3.2. Polyethylene Glycol (PEG) 20753.3.3. Polyvinyl Alcohol (PVA) 20753.3.4. Alginate 20753.3.5. Chitosan 20753.3.6. Other Polymers 20753.4. Other Strategies for Stabilization 20764. Methods of Vectorization of the Particles 20765. Structural and Physicochemical Characterization 20785.1. Size, Polydispersity, Shape, and SurfaceCharacterization20795.2. Structure of Ferro- or FerrimagneticNanoparticles20805.2.1. Ferro- and Ferrimagnetic Nanoparticles 20805.3. Use of Nanoparticles as Contrast Agents forMRI20825.3.1. High Anisotropy Model 20845.3.2. Small Crystal and Low Anisotropy EnergyLimit20855.3.3. Practical Interests of Magnetic NuclearRelaxation for the Characterization ofSuperparamagnetic Colloid20855.3.4. Relaxation of Agglomerated Systems 20856. Applications 20866.1. MRI: Cellular Labeling, Molecular Imaging(Inflammation, Apoptose, etc.)20866.2.

Reaction-rate theory: fifty years after Kramers

Abstract: The calculation of rate coefficients is a discipline of nonlinear science of importance to much of physics, chemistry, engineering, and biology. Fifty years after Kramers' seminal paper on thermally activated barrier crossing, the authors report, extend, and interpret much of our current understanding relating to theories of noise-activated escape, for which many of the notable contributions are originating from the communities both of physics and of physical chemistry. Theoretical as well as numerical approaches are discussed for single- and many-dimensional metastable systems (including fields) in gases and condensed phases. The role of many-dimensional transition-state theory is contrasted with Kramers' reaction-rate theory for moderate-to-strong friction; the authors emphasize the physical situation and the close connection between unimolecular rate theory and Kramers' work for weakly damped systems. The rate theory accounting for memory friction is presented, together with a unifying theoretical approach which covers the whole regime of weak-to-moderate-to-strong friction on the same basis (turnover theory). The peculiarities of noise-activated escape in a variety of physically different metastable potential configurations is elucidated in terms of the mean-first-passage-time technique. Moreover, the role and the complexity of escape in driven systems exhibiting possibly multiple, metastable stationary nonequilibrium states is identified. At lower temperatures, quantum tunneling effects start to dominate the rate mechanism. The early quantum approaches as well as the latest quantum versions of Kramers' theory are discussed, thereby providing a description of dissipative escape events at all temperatures. In addition, an attempt is made to discuss prominent experimental work as it relates to Kramers' reaction-rate theory and to indicate the most important areas for future research in theory and experiment.