Originator dynamics

We study the origin of evolution. Evolution is based on replication, mutation, and selection. But how does evolution begin? When do chemical kinetics turn into evolutionary dynamics? We propose "prelife" and "prevolution" as the logical precursors of life and evolution. Prelife generates sequences of variable length. Prelife is a generative chemistry that proliferates information and produces diversity without replication. The resulting "prevolutionary dynamics" have mutation and selection. We propose an equation that allows us to investigate the origin of evolution. In one limit, this "originator equation" gives the classical selection equation. In the other limit, we obtain "prelife." There is competition between life and prelife and there can be selection for or against replication. Simple prelife equations with uniform rate constants have the property that longer sequences are exponentially less frequent than shorter ones. But replication can reverse such an ordering. As the replication rate increases, some longer sequences can become more frequent than shorter ones. Thus, replication can lead to "reversals" in the equilibrium portraits. We study these reversals, which mark the transition from prelife to life in our model. If the replication potential exceeds a critical value, then life replicates into existence.     

Movement dynamics

Recently, several reports have suggested that the control of multi-joint limbs is mediated by reducing the number of degrees of freedom in redundant limbs. In addition, more insight has been gained into the constraints that are imposed on muscle activation patterns and joint rotations.     

Microtubule dynamics

A combination of biochemical, structural, and morphological analyses during the last 2 decades has shown that the cytoplasm of a cell is not a disorganized mass of jelly but a highly structured cell compartment formed of a cytoskeleton, one of which principal components are the microtubules. More recently, studies have revealed that microtubule cytoskeleton is not only well organized but highly dynamic, and that microtubule dynamics may be responsible for several cell functions such as chromosome segregation, cell morphogenesis, or intracytoplasmic organization.     

Replicator dynamics

Several evolutionary models in distinct biological fields—population genetics, population ecology, early biochemical evolution and sociobiology—lead independently to the same class of replicator dynamics.     

Mitotic dynamics

A new model for mitotic dynamics of eukaryotic cells is proposed. In the kinetochore mo-tor-midzone motor model two kinds of motors, the kinetochore motors and the midzone motors, play important roles in chromosome movement. Using this model the chromosome congression during prometaphase, the chromosome oscillation during metaphase and the chromatid segregation during anaphase are described in a unified way.     

Centromere dynamics

At the foundation of all eukaryotic kinetochores is a unique histone variant, known as CenH3 (centromere histone H3). We are starting to identify the histone chaperones responsible for CenH3 deposition at centromere DNA, and the mechanisms that restrict CenH3 from chromosome arms. The specialized nucleosome that contains CenH3 in place of canonical histone H3 lies at the interface between microtubules and chromosomes and directs kinetochore protein assembly. By contrast, pericentric chromatin is highly elastic and can stretch or recoil in response to microtubule shortening or growth in mitosis. The variety in histone modification is likely to play a key role in regulating the behavior of these distinct chromatin domains.     

Peroxisomal dynamics

Peroxisomes are a dynamic compartment in almost all eukaryotic cells and have diverse metabolic roles in response to environmental changes and cellular demands. The accompanying changes in enzyme content or abundance of peroxisomes are accomplished by dynamically operating membrane- and matrix-protein transport machineries. This review discusses recent progress in understanding peroxisomal proliferation and maintenance, insertion of peroxisomal membrane proteins, compartmentalization of peroxisomal matrix proteins and selective degradation of peroxisomes via pexophagy.     

Phytoplankton dynamics

We present a model of the phytoplankton dynamics. The distribution of the size of the phytoplankton aggregates is described by a non-linear transport equation that contains terms responsible for the growth of phytoplankton aggregates, their fragmentation and coagulation. We study asymptotic behaviour of moments of the solutions and we explain why phytoplankton tends to create large aggregates.     

Nucleosome dynamics

In the 30 years since the discovery of the nucleosome, our picture of it has come into sharp focus. The recent high-resolution structures have provided a wealth of insight into the function of the nucleosome, but they are inherently static. Our current knowledge of how nucleosomes can be reconfigured dynamically is at a much earlier stage. Here, recent advances in the understanding of chromatin structure and dynamics are highlighted. The ways in which different modes of nucleosome reconfiguration are likely to influence each other are discussed, and some of the factors likely to regulate the dynamic properties of nucleosomes are considered.     

Vascular dynamics

A study, using the four-electrode impedance plethysmograph system, was completed to evaluate simultaneous variations in conduction of upper and lower body segments relative to displacement of blood volume during change in body position. Measurements of cardiac output were compared with simultaneous results by dye dilution methods as a means of assessing the use of impedance techniques to determine cardiac output during tilt table studies. Two groups, 48 healthy private pilots and 22 patients with diabetes mellitus, were tested and the results were compared.Control and test heart rate values were higher in the afternoon than in the morning for the same healthy subjects, and the blood pressure and heart rate changes paralleled the variations in stroke volume and calf blood pulse changes. The results in the patients with diabetes differed markedly in terms of the magnitude of the cardiovascular changes and indicated the value of the tilt table in assessing fatigue in the circulatory system as a result of metabolic disturbance. The change from horizontal to 65 degree head up position in the patients with diabetes showed a marked fall in thoracic stroke and conductive volume in contrast to the minimal decrease observed in healthy subjects.Symbols resistivity, ohm cm - L length or distance between detecting electrodesE ₁-E ₂, cm - E voltage, volts - I current, amps - R ₀ segmental resistance between detecting electrodesE ₁-E ₂, ohms - V ₀ segmental volume equivalent to (L ²/R ₀), ml - V change in volume, ml - R change in resistance, ohms Terms Impedance plethysmography Measurement of change in volume due to variation in electrical resistance of a segment to a 50 or 120 kHz signal. The impedance at these frequencies is primarily resistive - Four electrodes Two electrodes for introduction of the reference signal to the examined segment and two electrodes for detecting variation in conduction of the signal - Conduction The reciprocal of resistance measured in mohs. - Conductive volume The volume defined byV ₀=(L ²/R ₀) containing electrolytes including whole blood and plasma This project was supported by Contract NAS4-1321, NASA Flight Research Center, Edwards, California, U.S.A.     

Eco-evolutionary dynamics

Evolutionary ecologists and population biologists have recently considered that ecological and evolutionary changes are intimately linked and can occur on the same time-scale. Recent theoretical developments have shown how the feedback between ecological and evolutionary dynamics can be linked, and there are now empirical demonstrations showing that ecological change can lead to rapid evolutionary change. We also have evidence that microevolutionary change can leave an ecological signature. We are at a stage where the integration of ecology and evolution is a necessary step towards major advances in our understanding of the processes that shape and maintain biodiversity. This special feature about ‘eco-evolutionary dynamics’ brings together biologists from empirical and theoretical backgrounds to bridge the gap between ecology and evolution and provide a series of contributions aimed at quantifying the interactions between these fundamental processes.     

Proteasome dynamics

Proteasomes are highly conserved multisubunit protease complexes and occur in the cyto- and nucleoplasm of eukaryotic cells. In dividing cells proteasomes exist as holoenzymes and primarily localize in the nucleus. During quiescence they dissociate into proteolytic core and regulatory complexes and are sequestered into motile cytosolic clusters. Proteasome clusters rapidly clear upon the exit from quiescence, where proteasome core and regulatory complexes reassemble and localize to the nucleus again. The mechanisms underlying proteasome transport and assembly are not yet understood. Here, I summarize our present knowledge about nuclear transport and assembly of proteasomes in yeast and project our studies in this eukaryotic model organism to the mammalian cell system. This article is part of a Special Issue entitled: Ubiquitin–Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf.     

Multiply accelerated ReaxFF molecular dynamics: coupling parallel replica dynamics with collective variable hyper dynamics

ABSTRACT

To tackle the time scales required to study complex chemical reactions, methods performing accelerated molecular dynamics are necessary even with the recent advancement in high-performance computing. A number of different acceleration techniques are available. Here we explore potential synergies between two popular acceleration methods – Parallel Replica Dynamics (PRD) and Collective Variable Hyperdynamics (CVHD), by analysing the speedup obtained for the pyrolysis of n-dodecane. We observe that PRD?+?CVHD provides additional speedup to CVHD by reaching the required time scales for the reaction at an earlier wall-clock time. Although some speedup is obtained with the additional replicas, we found that the effectiveness of the inclusion of PRD is depreciated for systems where there is a dramatic increase in reaction rates induced by CVHD. Similar observations were made in the simulation of ethylene-carbonate/Li system, which is inherently more reactive than pyrolysis, indicate that the speedup obtained via the combination of the two acceleration methods can be generalised to most practical chemical systems.     

OmpA: Gating and dynamics via molecular dynamics simulations

Outer membrane proteins (OMPs) of Gram-negative bacteria have a variety of functions including passive transport, active transport, catalysis, pathogenesis and signal transduction. Whilst the structures of ∼ 25 OMPs are currently known, there is relatively little known about their dynamics in different environments. The outer membrane protein, OmpA from Escherichia coli has been studied extensively in different environments both experimentally and computationally, and thus provides an ideal test case for the study of the dynamics and environmental interactions of outer membrane proteins. We review molecular dynamics simulations of OmpA and its homologues in a variety of different environments and discuss possible mechanisms of pore gating. The transmembrane domain of E. coli OmpA shows subtle differences in dynamics and interactions between a detergent micelle and a lipid bilayer environment. Simulations of the crystallographic unit cell reveal a micelle-like network of detergent molecules interacting with the protein monomers. Simulation and modelling studies emphasise the role of an electrostatic-switch mechanism in the pore-gating mechanism. Simulation studies have been extended to comparative models of OmpA homologues from Pseudomonas aeruginosa (OprF) and Pasteurella multocida (PmOmpA), the latter model including the periplasmic C-terminal domain.