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arXiv2014

The biomechanical properties of F1C pili

Uropathogenic Escherichia coli (UPEC) express various kinds of organelles, so-called pili or fimbriae, that mediate adhesion to host tissue in the urinary tract through specific receptor-adhesin interactions. The biomechanical properties of these pili have been considered important for the ability of bacteria to withstand shear forces from rinsing urine flows. Force measuring optical tweezers have been used to characterize individual organelles of F1C type expressed by UPEC bacteria with respect to such properties. Qualitatively, the force-vs.-elongation response was found to be similar to that of other types of helix-like pili expressed by UPEC, i.e. type 1, P, and S, with force-induced elongation in three regions of which one represents the important uncoiling mechanism of the helix-like quaternary structure. Quantitatively, the steady-state uncoiling force was assessed to 26.4(1.4) pN, which is similar to those of other pili (which range from 21 pN for SI to 30 pN for type 1). The corner velocity for dynamic response (1400 nm/s) was found to be larger than those of the other pili (400 -700 nm/s for S and P pili, and 6 nm/s for type 1). The kinetics were found to be faster, with a thermal opening rate of 17 Hz, a few times higher than S and P pili, and three orders of magnitude times higher than type 1. These data suggest that F1C pili are, like P and S pili, evolutionary-selected to primarily withstand the conditions expressed in the upper urinary tract.

physics.bio-ph↗

arXiv2014

Avoiding extinction by migration: The case of the head louse

The possibility of spreading by migration, colonizing new spatial domains suitable for development and reproduction, can substantially relieve a biological population from the risk of extinction. By means of a realistic computational model based on empirical data, we study this phenomenon for the human head louse, Pediculus humanus capitis. In particular, we show that a lice colony infesting a single isolated host is prone to extinction by stochastic population fluctuations within an interval of several months, while migration over a relatively small group of hosts in contact with each other is enough to insure the prevalence of the infestation for indefinitely long periods. We characterize the interplay of the size of the host group with the host-to-host contagion probability, which controls a transition between extinction of the lice population and a situation where the infestation is endemic.

q-bio.PE↗

arXiv2017

Do biological molecular machines act as Maxwell's demons?

The nanoscopic isothermal machines are not only energy but also information transducers. We show that the generalized fluctuation theorem with information creation and entropy reduction can be fulfilled for the enzymatic molecular machines with the stochastic dynamics, which offers a choice of the work performance in a variety of ways. A model of such dynamics, specified by a critical complex network, is investigated. The main conclusion of the study is that the processing of free energy has to be distinguished from the processing of organization, which we identify with an adequately defined thermodynamic variable. Maxwell's demon utilizes entropy reduction for creation of information, which, from the former point of view, may be used for a reduction of energy losses, hence ultimately, for the performance of work. From the latter point of view, however, it can be used for other purposes, for example molecular recognition. This can be the case of biological molecular machines. From the biological perspective, the ascertainment is important, that the information creation and storage take place in the long lasting transient stages before completing the free energy transduction cycles. From a broader physical perspective, a supposition could be of special importance, that information is a change of organization, the thermodynamic function of state of the system.

physics.bio-ph↗

arXiv2015

Enhancing light-harvesting power with coherent vibrational interactions: a quantum heat engine picture

Recent evidence suggests that quantum effects may have functional importance in biological light-harvesting systems. Along with delocalized electronic excitations, it is now suspected that quantum coherent interactions with certain near-resonant vibrations may contribute to light-harvesting performance. However, the actual quantum advantage offered by such coherent vibrational interactions has not yet been established. We investigate a quantum design principle, whereby coherent exchange of single energy quanta between electronic and vibrational degrees of freedom can enhance a light-harvesting system's power above what is possible by thermal mechanisms alone. We present a prototype quantum heat engine which cleanly illustrates this quantum design principle, and quantify its quantum advantage using thermodynamic measures of performance. We also demonstrate the principle's relevance in parameter regimes connected to natural light-harvesting structures.

physics.chem-ph↗

arXiv2014

Computational studies of biomembrane systems: Theoretical considerations, simulation models, and applications

This chapter summarizes several approaches combining theory, simulation and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane mediated interactions, attraction between transmembrane proteins, and aggregation in biomembranes leading to large superstructures such as the light harvesting complex of green plants. After a general overview of theoretical considerations and continuum theory of lipid membranes we introduce different options for simulations of biomembrane systems, addressing questions such as: What can be learned from generic models? When is it expedient to go beyond them? And what are the merits and challenges for systematic coarse graining and quasi-atomistic coarse grained models that ensure a certain chemical specificity?

physics.bio-ph↗

arXiv2015

Effects of aging in catastrophe on the steady state and dynamics of a microtubule population

Several independent observations have suggested that catastrophe transition in microtubules is not a first-order process, as is usually assumed. Recent {\it in vitro} observations by Gardner et al.[ M. K. Gardner et al., Cell {\bf147}, 1092 (2011)] showed that microtubule catastrophe takes place via multiple steps and the frequency increases with the age of the filament. Here, we investigate, via numerical simulations and mathematical calculations, some of the consequences of age dependence of catastrophe on the dynamics of microtubules as a function of the aging rate, for two different models of aging: exponential growth, but saturating asymptotically and purely linear growth. The boundary demarcating the steady state and non-steady state regimes in the dynamics is derived analytically in both cases. Numerical simulations, supported by analytical calculations in the linear model, show that aging leads to non-exponential length distributions in steady state. More importantly, oscillations ensue in microtubule length and velocity. The regularity of oscillations, as characterized by the negative dip in the autocorrelation function, is reduced by increasing the frequency of rescue events. Our study shows that age dependence of catastrophe could function as an intrinsic mechanism to generate oscillatory dynamics in a microtubule population, distinct from hitherto identified ones.

q-bio.SC↗

arXiv2014

Characterising two-pathogen competition in spatially structured environments

Different pathogens spreading in the same host population often generate complex co-circulation dynamics because of the many possible interactions between the pathogens and the host immune system, the host life cycle, and the space structure of the population. Here we focus on the competition between two acute infections and we address the role of host mobility and cross-immunity in shaping possible dominance/co-dominance regimes. Host mobility is modelled as a network of traveling flows connecting nodes of a metapopulation, and the two-pathogen dynamics is simulated with a stochastic mechanistic approach. Results depict a complex scenario where, according to the relation among the epidemiological parameters of the two pathogens, mobility can either be non-influential for the competition dynamics or play a critical role in selecting the dominant pathogen. The characterisation of the parameter space can be explained in terms of the trade-off between pathogen's spreading velocity and its ability to diffuse in a sparse environment. Variations in the cross-immunity level induce a transition between presence and absence of competition. The present study disentangles the role of the relevant biological and ecological factors in the competition dynamics, and provides relevant insights into the spatial ecology of infectious diseases.

q-bio.PE↗

arXiv2014

Correlations between Chondroitin Sulfate Physicochemical Properties and its in-vitro Absorption and Anti-inflammatory Activity

Here, we investigated the influence of physicochemical characteristics of chondroitin sulfate (CS) on its in vitro absorption and anti-inflammatory activity. We used eight different synthetic and natural CS samples with a range of molecular weights (7-35 kDa) and sulfation patterns. Our studies indicate that the absorption of CS is moderately correlated to percentage of chondroitin-6-sulfate while the anti-inflammatory activity may be weakly related to the molecular weight and the amount of total sulfation in the samples. Our in vitro studies could provide helpful screening tools for quick and effective evaluation of CS samples as a preliminary step towards in vivo studies.

q-bio.TO↗

arXiv2014

Vibration-assisted coherent excitation energy transfer in a detuning system

The roles of the vibration motions played in the excitation energy transfer process are studied. It is found that a strong coherent transfer in the hybrid system emerges when the detuning between the donor and the acceptor equals the intrinsic frequency of the vibrational mode, and as a result the energy can be transferred into the acceptor much effectively. Three cases of the donor and the acceptor coupling with vibrational modes are investigated respectively. We find that the quantum interference between the two different transfer channels via the vibrational modes can affects the dynamics of the system significantly.

physics.bio-ph↗

arXiv2014

X-optogenetics and U-optogenetics: Feasibility and Possibilities

To address these limitations of optogenetics, here we propose two new methods for optogenetic stimulation. The first is x-optogenetics, which uses visible light-emitting nanophosphors stimulated by focused x-rays. This idea is not new but the application to optogenetics is novel. X-rays can penetrate much more deeply than infrared light and could allow for nerve cell stimulation in any part of the brain. In this paper, we discuss the feasibility and possibilities of such a method by describing the advances in nanomaterials, x-ray focusing, and x-ray sources. Also, we discuss concerns when dealing with x-rays such as radiation dosage. Through the use of quantities and assumptions backed by recent literature, manufacturer specifications, and personal correspondence, a full feasibility analysis of x-optogenetics is completed. The second proposed method we explore is u-optogenetics, which is the application of sonoluminescence to optogenetics. Such a technique uses ultrasound waves instead of x-rays to induce light emission, so there would be no introduction of radiation. However, the penetration depth of ultrasound is less than that of x-ray. The key issues affecting feasibility are laid out for further investigation into both x-optogenetics and u-optogenetics.

physics.bio-ph↗

arXiv2014

pyFRET: A Python Library for Single Molecule Fluorescence Data Analysis

Single molecule Förster resonance energy transfer (smFRET) is a powerful experimental technique for studying the properties of individual biological molecules in solution. However, as adoption of smFRET techniques becomes more widespread, the lack of available software, whether open source or commercial, for data analysis, is becoming a significant issue. Here, we present pyFRET, an open source Python package for the analysis of data from single-molecule fluorescence experiments from freely diffusing biomolecules. The package provides methods for the complete analysis of a smFRET dataset, from burst selection and denoising, through data visualisation and model fitting. We provide support for both continuous excitation and alternating laser excitation (ALEX) data analysis. pyFRET is available as a package downloadable from the Python Package Index (PyPI) under the open source three-clause BSD licence, together with links to extensive documentation and tutorials, including example usage and test data. Additional documentation including tutorials is hosted independently on ReadTheDocs. The code is available from the free hosting site Bitbucket. Through distribution of this software, we hope to lower the barrier for the adoption of smFRET experiments by other research groups and we encourage others to contribute modules for specific analysis needs.

cs.CE↗

arXiv2014

Stochastic biophysical modeling of irradiated cells

The paper presents a computational stochastic model of virtual cells irradiation, based on Quasi-Markov Chain Monte Carlo method and using biophysical input. The model is based on a stochastic tree of probabilities for each cell of the entire colony. Biophysics of the cells is described by probabilities and probability distributions provided as the input. The adaptation of nucleation and catastrophe theories, well known in physics, yields sigmoidal relationships for carcinogenic risk as a function of the irradiation. Adaptive response and bystander effect, incorporated into the model, improves its application. The results show that behavior of virtual cells can be successfully modeled, e.g. cancer transformation, creation of mutations, radioadaptation or radiotherapy. The used methodology makes the model universal and practical for simulations of general processes. Potential biophysical curves and relationships are also widely discussed in the paper. However, the presented theoretical model does not describe the real cells and tissues. Also the exposure geometry (e.g., uniform or non-uniform exposure), type of radiation (e.g., X-rays, gamma rays, neutrons, heavy ions, etc.) as well as microdosimetry are not presently addressed. The model is focused mainly on creation of general and maximal wide mathematical description of irradiated hypothetical cells treated as complex physical systems.

physics.bio-ph↗

arXiv2014

Physical constraints for the Stoneham model for light-dependent magnetoreception

A new biophysical model for magnetoreception in migratory birds has recently been proposed by Stoneham et al. In this photo-induced radical pair (RP) model the signal transduction mechanism was physical rather than chemical in nature, as otherwise generally assumed in the literature. The proposal contains a magnetosensor and a signal transduction mechanism. The sensor would be an electric dipole related to a long lived triplet state of an RP. This makes it sensitive to the geomagnetic field via the Zeeman interaction. The field of the electric dipole moment would then promote isomerization from cis-to-trans in the retinal of a nearby rhodopsin. This would trigger the neuronal signal. Here we gather several observations from different works that constrain the feasibility of this physical model. In particular we argue that the perturbation of rhodopsin by a local electric field from a nearby electric dipole (10^6 V/m) cannot modify the field in the binding pocket of rhodopsin (10^9 V/m) sufficiently to trigger the isomerization of cis-retinal. The dipole field is much weaker than those from other sources in the vicinity which are known not to promote isomerization.

physics.bio-ph↗

arXiv2014

Virtual reality based approach to protein heavy-atom structure reconstruction

A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central alpha-carbon coordinates. We employ advances in virtual reality to address the problem. The outcome is a 3D visualisation based technique where all the heavy backbone and side chain atoms are treated on equal footing, in terms of the C-alpha coordinates. Each heavy atom can be visualised on the surfaces of the different two-spheres, that are centered at the other heavy backbone and side chain atoms. In particular, the rotamers are visible as clusters which display strong dependence on the underlying backbone secondary structure. Our method easily detects those atoms in a crystallographic protein structure which have been been likely misplaced. Our approach forms a basis for the development of a new generation, visualisation based side chain construction, validation and refinement tools. The heavy atom positions are identified in a manner which accounts for the secondary structure environment, leading to improved accuracy over existing methods.

q-bio.BM↗

arXiv2014

WHAT IS LIFE - Sub-cellular Physics of Live Matter

This is a set of lectures that I presented at the Les Houches 2014 Summer School "Topological Aspects in Condensed Matter Physics". The lectures are an introduction to physics of proteins. To physicists, and by a physicist. My lectures at les Houches were also celebration of the anniversary of Schroedinger's 1944 lectures, and for that reason I decided to share my title with his book.

cond-mat.soft↗

arXiv2014

AADNMR: A Simple Method for Rapid Identification of Bacterial/Mycobacterial Infections in Antibiotic Treated Peritoneal Dialysis Effluent Samples for Diagnosis of Infectious Peritonitis

An efficient method is reported for rapid identification of bacterial or mycobacterial infection in a suspected clinical/biological sample. The method is based on the fact that the ring methylene protons of cyclic fatty acids (constituting the cell membrane of several species of bacteria and mycobacteria) resonate specifically between -0.40 and 0.68 ppm region of the 1H NMR spectrum. These cyclic fatty acids are rarely found in the eukaryotic cell membranes. Therefore, the signals from cyclic ring moiety of these fatty acids can be used as markers (a) for the identification of bacterial and mycobacterial infections and (b) for differential diagnosis of bacterial and fungal infections. However, these microbial fatty acids when present inside the membrane are not easily detectable by NMR owing to their fast T2 relaxation. Nonetheless, the problem can easily be circumvented if these fatty acids become suspended in solution. This has been achieved by abolishing the membrane integrity using broad spectrum antibiotics (including ampicillin). The suspended fatty acids are then detected by NMR to probe the infection. Therefore, the method has been given the name AADNMR i.e. Add Antibiotic to Detect by NMR. The method has been tested here using both Gram positive and Gram negative bacterial strains and finally the utility of method is demonstrated for discriminating bacterial and fungal infections to aid timely diagnosis of infectious peritonitis (a life threatening complication associated with prolonged peritoneal dialysis).

physics.bio-ph↗

arXiv2014

Information processing in living systems

Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been possible to measure, directly, the flow of information in biological networks, or more generally where information theoretic ideas have been used to guide the analysis of experiments. Systems of interest range from single molecules (the sequence diversity in families of proteins) to groups of organisms (the distribution of velocities in flocks of birds), and all scales in between. Many of these analyses are motivated by the idea that biological systems may have evolved to optimize the gathering and representation of information, and we review the experimental evidence for this optimization, again across a wide range of scales.

q-bio.QM↗

arXiv2014

Widefield two-photon excitation without scanning: live cell microscopy with high time resolution and low photo-bleaching

We demonstrate fluorescence imaging by two-photon excitation without scanning in biological specimens as previously described by Hwang and co-workers, but with an increased field size and with framing rates of up to 100 Hz. During recordings of synaptically-driven Ca$^{2+}$ events in primary rat neurone cultures loaded with the fluorescent Ca$^{2+}$ indicator Fluo-4 AM, we have observed greatly reduced photo-bleaching in comparison with single-photon excitation. This method, which requires no costly additions to the microscope, promises to be useful for work where high time-resolution is required.

physics.bio-ph↗