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arXiv2013

Hole Conductivity in Heterogeneous DNA Fragments

The characteristics of cation radical (hole) migration in heterogeneous DNA were investigated on the basis of Kubo formula, in which correlation functions were obtained from solutions of systems of Bogoliubov hierarchy. The cutting of Bogoliubov hierarchy was carried out by excepting correlations of the third and higher order. The obtained system of non-linear differential equations was investigated both analytically and numerically. The environment polarization, caused by interaction of holes with base pairs vibrations, was shown to play the key role in transport processes. The energy of the interaction can ten-fold exceed vibration energy. The transfer rate between adjacent DNA bases in one-dimensional case was shown to be almost independent of the nature and behavior of more distant pairs. The charge probability amplitude oscillates in the picosecond timescale. Nonetheless, the rates of hole transfer, obtained by averaging over these oscillations, turned out to be very close to the experimental data. The calculated dependence of the hole transfer rate between two guanine bases on the number of intervening adenine bases was also in good agreement with the experimental data. Besides, the temperature dependence of the transfer rate was investigated. Hopping mechanism was shown to make the main contribution to the hole transport process at 300 K.

cond-mat.other↗

arXiv2013

In vitro toxicity of nanoceria: effect of coating and stability in biofluids

Due to the increasing use of nanometric cerium oxide in applications, concerns about the toxicity of these particles have been raised and have resulted in a large number of investigations. We report here on the interactions between 7 nm anionically charged cerium oxide particles and living mammalian cells. By a modification of the particle coating including low-molecular weight ligands and polymers, two generic behaviors are compared: particles coated with citrate ions that precipitate in biofluids and particles coated with poly(acrylic acid) that are stable and remain nanometric. We find that nanoceria covered with both coating agents are taken up by mouse fibroblasts and localized into membrane-bound compartments. However, flow cytometry and electron microscopy reveal that as a result of their precipitation, citrate-coated particles interact more strongly with cells. At cerium concentration above 1 mM, only citrate-coated nanoceria (and not particles coated with poly(acrylic acid)) display toxicity and moderate genotoxicity. The results demonstrate that the control of the surface chemistry of the particles and its ability to prevent aggregation can affect the toxicity of nanomaterials.

physics.bio-ph↗

arXiv2013

Back-scatter based whispering gallery mode sensing

Whispering gallery mode biosensors allow selective unlabelled detection of single proteins and, combined with quantum limited sensitivity, the possibility for noninvasive realtime observation of motor molecule motion. However, to date technical noise sources, most particularly low frequency laser noise, have constrained such applications. Here we introduce a new technique for whispering gallery mode sensing based on direct detection of back-scattered light. This experimentally straightforward technique is immune to frequency noise in principle, and further, acts to suppress thermorefractive noise. We demonstrate 27 dB of frequency noise suppression, eliminating frequency noise as a source of sensitivity degradation and allowing an absolute frequency shift sensitivity of 76 kHz. Our results open a new pathway towards single molecule biophysics experiments and ultrasensitive biosensors.

physics.optics↗

arXiv2013

Numerical Simulation of Folding and Unfolding of Proteins

The thesis examines in detail the folding and unfolding processes of a number of proteins including hbSBD, DDLNF4, single and multi Ubiquitin. Using simplified coarse-grained off-lattice Go model and CD experiments we have shown the two-state behavior of hbSBD protein. It was shown that refolding pathways of single Ubiquitin depend on what end is anchored to the surface. Namely, the fixation of the N-terminal changes refolding pathways but anchoring the C-terminal leaves them unchanged. Interestingly, the end fixation has no effect on multi-domain Ubiquitin. Using the Go modeling and all-atom models with explicit water, we have studied the mechanical unfolding mechanism of DDFLN4 in detail. We predict that, contrary to the AFM experiments, an additional unfolding peak would occur at the end-to-end $ΔR \approx 1.5 $nm in the force-extension curve. Our study reveals the important role of non-native interactions which are responsible for a peak located at $ΔR \approx 22 $nm. This peak can not be encountered by the Go models in which the non-native interactions are neglected. Our finding may stimulate further experimental and theoretical studies on this protein. The cooperativity of denaturation transition was investigated using lattice and off-latice models. Our studies reveal that the sharpness of the transition enhances as the number of amino acids grows. The corresponding scaling behavior is governed by an universal critical exponent. A new force replica exchange (RE) method was developed for efficient configuration sampling of biomolecules pulled by an external mechanical force. Contrary to the standard temperature RE, the exchange is carried out between different forces (replicas). Our method was successfully applied to study thermodynamics of a three-domain Ubiquitin.

physics.bio-ph↗

arXiv2013

Protein folding tames chaos

Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to theoretical modeling and computer simulations. The present work introduces molecular nonlinear dynamics (MND), or molecular chaotic dynamics, as a theoretical framework for describing and analyzing protein folding. We unveil the existence of intrinsically low dimensional manifolds (ILDMs) in the chaotic dynamics of folded proteins. Additionally, we reveal that the transition from disordered to ordered conformations in protein folding increases the transverse stability of the ILDM. Stated differently, protein folding reduces the chaoticity of the nonlinear dynamical system, and a folded protein has the best ability to tame chaos. Additionally, we bring to light the connection between the ILDM stability and the thermodynamic stability, which enables us to quantify the disorderliness and relative energies of folded, misfolded and unfolded protein states. Finally, we exploit chaos for protein flexibility analysis and develop a robust chaotic algorithm for the prediction of Debye-Waller factors, or temperature factors, of protein structures.

q-bio.BM↗

arXiv2013

The role of blood circulatory system in thermal regulation of animals explained by entropy production analysis

A novel model of thermal regulation of homoeothermic animals has been implemented. The model is based on a non-equilibrium thermodynamic approach which introduces entropy balance and the rate of entropy generation as a formulation of The Second Law. The model explains linear correlation between an animals skin and environment temperatures using the first principles and demonstrates the role of blood circulation in the thermoregulation of homoeothermic animals.

q-bio.OT↗

arXiv2013

Thermodynamic properties of microbian populations on biological membranes

In this work we to develop a general statistical mechanic formalism to study systems restricted to surfaces of revolution, these are a very well model to study the termodinamical properties of microbiological systems and macromolecules lies on biological membranes such as cellular well.

cond-mat.soft↗

arXiv2013

Imaging electrical activity of neurons with metamaterial nanosensors

A technology for recording electrical activity of large neuron populations at arbitrary depth in brain tissues with less than cell spatial and millisecond temporal resolutions was the most craving dream of neuroscientists and a long pursued goal of engineers for decades. Even though many imaging techniques have been devised up to date, none of them is capable to deliver either quantitatively valid data nor able to meet contradictory requirements posed for sensors to be safe, non-invasive and reliably working either within cultured cell populations or during chronic implantations in vivo. In my research project, I design and justify a novel nanobiosensors, capable to detect and optically report the electric fields across cellular membrane and investigate properties of that specially engineered plasmonic nanoantennas. In the following literature survey, I observe the current state of electrophysiology methods and after recalling the basics of fluorescence, discuss benefits and drawbacks of today's voltage sensitive labelling and electric fields imaging methods. This review is wrapped up by a brief outlook of prospective applications of this technology.

physics.bio-ph↗

arXiv2013

On the crucial features of a single-file transport model for ion channels

It has long been accepted that the multiple-ion single-file transport model is appropriate for many kinds of ion channels. However, most of the purely theoretical works in this field did not capture all of the important features of the realistic systems. Nowadays, large-scale atomic-level simulations are more feasible. Discrepancy between theories, simulations and experiments are getting obvious, enabling people to carefully examine the missing parts of the theoretical models and methods. In this work, it is attempted to find out the essential features that such kind of models should possess, in order that the physical properties of an ion channel be adequately reflected.

physics.bio-ph↗

arXiv2013

Fluctuations in lipid bilayers: Are they understood?

We review recent computer simulation studies of undulating lipid bilayers. Theoretical interpretations of such fluctuating membranes are most commonly based on generalized Helfrich-type elastic models, with additional contributions of local "protrusions" and/or density fluctuations. Such models provide an excellent basis for describing the fluctuations of tensionless bilayers in the fluid phase at a quantitative level. However, this description is found to fail for membranes in the gel phase and for membranes subject to high tensions. The fluctuations of tilted gel membranes show a signature of the modulated ripple structure, which is a nearby phase observed in the pretransition regime between the fluid and tilted gel state. This complicates a quantitative analysis on mesoscopic length scales. In the case of fluid membranes under tension, the large-wavelength fluctuation modes are found to be significantly softer than predicted by theory. In the latter context, we also address the general problem of the relation between frame tension and the fluctuation tension, which has been discussed somewhat controversially in recent years. Simulations of very simple model membranes with fixed area show that the fluctuations should be controlled by the frame tension, and not by the internal tension.

physics.bio-ph↗

arXiv2013

An alternative to the breeder's and Lande's equations

The breeder's equation is a cornerstone of quantitative genetics and is widely used in evolutionary modeling. The equation which reads R=h^{2}S relates response to selection R (the mean phenotype of the progeny) to the selection differential S (mean phenotype of selected parents) through a simple proportionality relation. The validity of this relation however relies strongly on the normal (Gaussian) distribution of parent's genotype which is an unobservable quantity and cannot be ascertained. In contrast, we show here that if the fitness (or selection) function is Gaussian, an alternative, exact linear equation in the form of R'=j^{2}S' can be derived, regardless of the parental genotype distribution. Here R' and S' stand for the mean phenotypic lag behind the mean of the fitness function in the offspring and selected populations. To demonstrate this relation, we derive the exact functional relation between the mean phenotype in the selected and the offspring population and deduce all cases that lead to a linear relation between these quantities. These computations, which are confirmed by individual based numerical simulations, generalize naturally to the multivariate Lande's equation Δ\mathbf{\bar{z}}=GP^{-1}\mathbf{S} .

q-bio.PE↗

arXiv2013

Top-Down Mass Spectrometry Imaging of Intact Proteins by LAESI FT-ICR MS

Laser Ablation Electrospray Ionization is a recent development in mass spectrometry imaging. It has been shown that lipids and small metabolites can be imaged in various samples such as plant material, tissue sections or bacterial colonies without anysample pre-treatment. Further, laser ablation electrospray ionization has been shown to produce multiply charged protein ions from liquids or solid surfaces. This presents a means to address one of the biggest challenges in mass spectrometry imaging; the identification of proteins directly from biological tissue surfaces. Such identification is hindered by the lack of multiply charged proteins in common MALDI ion sources and the difficulty of performing tandem MS on such large, singly charged ions. We present here top-down identification of intact proteins from tissue with a LAESI ion source combined with a hybrid ion-trap FT-ICR mass spectrometer. The performance of the system was first tested with a standard protein with ECD and IRMPD fragmentation to prove the viability of LAESI FT-ICR for top-down proteomics. Finally, the imaging of a tissue section was performed, where a number of intact proteins were measured and the hemoglobin α chain was identified directly from tissue using collision-induced dissociation and infrared multiphoton dissociation fragmentation.

physics.bio-ph↗

arXiv2013

Monte Carlo study elucidates the type 1/type 2 choice in apoptotic death signaling in normal and cancer cells

Apoptotic cell death is coordinated through two distinct (type 1 and type 2) intracellular signaling pathways. How the type 1/type 2 choice is made remains a fundamental problem in the biology of apoptosis and has implications for apoptosis related diseases and therapy. We study the problem of type 1/type 2 choice in silico utilizing a kinetic Monte Carlo model of cell death signaling. Our results show that the type 1/type 2 choice is linked to deterministic versus stochastic cell death activation, elucidating a unique regulatory control of the apoptotic pathways. Consistent with previous findings, our results indicate that caspase 8 activation level is a key regulator of the choice between deterministic type 1 and stochastic type 2 pathways, irrespective of cell types. Expression levels of signaling molecules downstream also regulate the type 1/type 2 choice. A simplified model of DISC clustering elucidates the mechanism of increased active caspase 8 generation, and type 1 activation, in cancer cells having increased sensitivity to death receptor activation. We demonstrate that rapid deterministic activation of the type 1 pathway can selectively target those cancer cells, especially if XIAP is also inhibited; while inherent cell-to-cell variability would allow normal cells stay protected.

q-bio.MN↗

arXiv2013

Identifying all irreducible conserved metabolite pools in genome-scale metabolic networks: a general method and the case of Escherichia coli

The stoichiometry of metabolic networks usually gives rise to a family of conservation laws for the aggregate concentration of specific pools of metabolites, which not only constrain the dynamics of the network, but also provide key insight into a cell's production capabilities. When the conserved quantity identifies with a chemical moiety, extracting all such conservation laws from the stoichiometry amounts to finding all integer solutions to an NP-hard programming problem. Here we propose a novel and efficient computational strategy that combines Monte Carlo, message passing, and relaxation algorithms to compute the complete set of irreducible integer conservation laws of a given stoichiometric matrix, also providing a certificate for correctness and maximality of the solution. The method is deployed for the analysis of the complete set of irreducible integer pools of two large-scale reconstructions of the metabolism of the bacterium Escherichia coli in different growth media. In addition, we uncover a scaling relation that links the size of the irreducible pool basis to the number of metabolites, for which we present an analytical explanation.

q-bio.MN↗

arXiv2013

Predicting unobserved exposures from seasonal epidemic data

We consider a stochastic Susceptible-Exposed-Infected-Recovered (SEIR) epidemiological model with a contact rate that fluctuates seasonally. Through the use of a nonlinear, stochastic projection, we are able to analytically determine the lower dimensional manifold on which the deterministic and stochastic dynamics correctly interact. Our method produces a low dimensional stochastic model that captures the same timing of disease outbreak and the same amplitude and phase of recurrent behavior seen in the high dimensional model. Given seasonal epidemic data consisting of the number of infectious individuals, our method enables a data-based model prediction of the number of unobserved exposed individuals over very long times.

q-bio.PE↗

arXiv2013

Physarum wires: Self-growing self-repairing smart wires made from slime mould

We report experimental laboratory studies on developing conductive pathways, or wires, using protoplasmic tubes of plasmodium of acellular slime mould Physarum polycephalum. Given two pins to be connected by a wire, we place a piece of slime mould on one pin and an attractant on another pin. Physarum propagates towards the attract and thus connects the pins with a protoplasmic tube. A protoplasmic tube is conductive, can survive substantial over-voltage and can be used to transfer electrical current to lightning and actuating devices. In experiments we show how to route Physarum wires with chemoattractants and electrical fields. We demonstrate that Physarum wire can be grown on almost bare breadboards and on top of electronic circuits. The Physarum wires can be insulated with a silicon oil without loss of functionality. We show that a Physarum wire self-heals: end of a cut wire merge together and restore the conductive pathway in several hours after being cut. Results presented will be used in future designs of self-growing wetware circuits and devices, and integration of slime mould electronics into unconventional bio-hybrid systems.

physics.bio-ph↗

arXiv2013

Robust signals from a quantum-based magnetic compass sensor

A quantum-based magnetic compass sensor, mediated through radical pair reactions, has been suggested to underlie the sensory ability of migrating birds to receive directional information from the geomagnetic field. Here we extend the currently available models by considering the effects of slow fluctuations in the nuclear spin environment on the directional signal. We quantitatively evaluate the robustness of signals under fluctuations on a timescale longer than the lifetime of a radical pair, utilizing two models of radical pairs. Our results suggest design principles for building a radical-pair based compass sensor that is both robust and highly directional sensitive.

physics.bio-ph↗

arXiv2013

Nanoscale elucidation of Na,K-ATPase isoforms in dendritic spines

The dimensions of neuronal synapses suggest that optical super-resolution imaging methods are necessary for thorough investigation of protein distributions and interactions. Nanoscopic evaluation of neuronal samples has presented practical hurdles, but advancing methods are making synaptic protein topology and quantification measurements feasible. This work explores the application of Photoactivated Localization Microscopy (PALM) pointilistic super-resolution imaging for investigation of the membrane bound sodium pump, the Na,K-ATPase, in matured neurons. Two isoforms of the sodium pump (ATP1a1 and ATP1a3) were studied in cultured neurons using the PALM-compatible fluorescent proteins PAGFP and mEos. Nanoscopic imaging reveals a compartmentalized distribution of sodium pumps in dendritic spines. Several nanoclusters of pumps are typically found in the spine head and relatively few in the spine neck. The density of sodium pumps was estimated from a quantification of detected single molecules to 600-800 pump copies/um2 in the spine heads. We have utilized PALM for dissection of nanoscale localization in mature cultured neurons and demonstrated similar topology and quantification estimates with PAGFP and mEos. PALM topology assessments of the sodium pump appeared similar to previous STED studies, though quantification estimates varied notably, implying that sample labeling strategies and choice of nanoscopic imaging method are critical factors for correct quantification.

physics.bio-ph↗