Searcharxiv⌕ Search

SEARCH · Searcharxiv

Results for “physics.bio-ph”

Search indexed arXiv papers on artificial intelligence, large language models, computer vision and robotics. Read source abstracts and follow links to arXiv.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12Linked to original sources
arXiv2013

Towards a continuum model for particle-induced velocity fluctuations in suspension flow through a stenosed geometry

Non-particulate continuum descriptions allow for computationally efficient modeling of suspension flows at scales that are inaccessible to more detailed particulate approaches. It is well known that the presence of particles influences the effective viscosity of a suspension and that this effect has thus to be accounted for in macroscopic continuum models. The present paper aims at developing a non-particulate model that reproduces not only the rheology but also the cell-induced velocity fluctuations, responsible for enhanced diffusivity. The results are obtained from a coarse-grained blood model based on the lattice Boltzmann method. The benchmark system comprises a flow between two parallel plates with one of them featuring a smooth obstacle imitating a stenosis. Appropriate boundary conditions are developed for the particulate model to generate equilibrated cell configurations mimicking an infinite channel in front of the stenosis. The averaged flow field in the bulk of the channel can be described well by a non-particulate simulation with a matched viscosity. We show that our proposed phenomenological model is capable to reproduce many features of the velocity fluctuations.

cond-mat.soft↗
arXiv2013

Rotating-crystal Malaria Diagnosis: Pre-clinical validation

Improving the efficiency of malaria diagnosis is one of the main goals of current malaria research. We have recently developed a magneto-optical (MO) method which allows high-sensitivity detection of malaria pigment (hemozoin) crystals via their magnetically induced rotation in blood. Here, we validate this technique on laboratory derived blood samples infected with \textit{Plasmodium falciparum}. Using two parasite cultures, the first containing mostly ring stages and the second corresponding to the end of the parasite life cycle, we demonstrate that our novel method can detect parasite densities as low as $\sim$40 and $\sim$10\,parasites per microliter of blood for ring and schizont stage parasites, respectively. This detection limit exceeds the performance of rapid diagnostic tests and competes with the threshold achievable by light microscopic observation of blood smears. Our method can be performed with as little as 50\,microliter of capillary blood and is sensitive to the presence of hemozoin micro-crystals down to ppm concentrations. The device, designed to a portable format for clinical and in-field tests, requires no special training of the operator or specific reagents, except for an inexpensive lysis solution to release intracellular hemozoin. Beyond diagnostics, this technique may offer an efficient tool to study hemozoin formation, trace hemozoin kinetics in the body and test susceptibility/resistance of parasites to new antimalarial drugs inhibiting hemozoin formation.

physics.med-ph↗
arXiv2013

Towards Hybrid Artificial-Slime Mould Devices

The plasmodium of the slime mould Physarum polycephalum has recently received significant attention for its value as a highly malleable amorphous computing substrate. In laboratory-based experiments, micro- and nanoscale artificial circuit components were introduced into the P. polycephalum plasmdodium to investigate the electrical properties and computational abilities of hybridised slime mould. It was found through a combination of imaging techniques and electrophysiological measurements that P. polycephalum is able to internalise a range of electrically active nanoparticles, assemble them in vivo and distribute them around the plasmodium. Hybridised plasmodium is able to form biomorphic mineralised networks, both inside the living plasmodium and the empty trails left in its wake by taxis, both of which facilitate the transmission of electricity. Hybridisation also alters the bioelectrical activity of the plasmodium and likely influences its information processing capabilities. It was concluded that hybridised slime mould is a suitable substrate for producing functional unconventional computing devices.

cs.ET↗
arXiv2013

Modèle théorique de la contraction musculaire squelettique : ressorts entropiques, processus stochastiques et mécanique classique (A theoretical model of skeletal muscular contraction : entropic springs, stochastic processes and classical mechanics)

The model analyzes the muscle fiber as a deformable system for which experimental data are determinated with the help of the laws of Newtonian mechanic. The model predicts the four transient phases for the shortening of a muscle fiber according to a force or length step. The model shows, on the one hand, the importance of the viscosity during the first phase of these two types of step and, secondly, the interdependence of the six other phases towards a bimodal state after disappearance of actions due to viscosity. The model provides an interpretation for the behavior of a fiber with shortening staircase. The model is consistent with experimental data during temperature changes or various structural alterations.

q-bio.TO↗
arXiv2013

Study on Antibody-Virus Interaction using Molecular Dynamics: Two Dimensional Simulation on Immunoglobulin Reaction against Human Papillomavirus

Human Papillomavirus (HPV) has been known as one of the cause of virus-induced cancer such as cervical cancer and carcinoma. Among other types of cancer, this type has higher chance in being prevented earlier. The main idea is to eradicate the virus as soon as it enters the body by marking it with antibodies; signaling the immune system to dispose of it. However, the antibodies must be trained to recognize the virus. They can be trained by inserting an object similar to the virus allowing them to learn to recognize and surround the inserted object. In response to this, molecular dynamics simulation was chosen to study the antibody-virus interaction. In this work, two-dimensional case that involves HPV and immunoglobulin (Ig) was studied and observed. Two types of objects will be defined; one stands for HPV while another stands for antibodies. The interaction between the two objects will be governed by two forces; Coulomb force and repulsive contact force. Through the definition of some rules and condition, the antibodies' motion was observed. The influence of antibody concentration, and the antibody's type and their appearance sequence were observed both quantitatively and visually. Keywords: antibody-virus interaction, molecular dynamics, HPV, immunoglobulin.

q-bio.CB↗
arXiv2013

Multi-Shell Ankylography

Three-dimensional (3D) imaging techniques appeal to a broad range of scientific and industrial applications. Typically, projection slice theorem enables multiple two-dimensional (2D) projections of an object to be combined in the Fourier domain to yield a 3D image. However, traditional techniques require a significant number of projections. The significant number of views required in conventional tomography not only complicates such imaging modalities, but also limits their ability to image samples that are sensitive to radiation dose or are otherwise unstable in time. In this work, we demonstrate through numerical simulations and an eigenvalue analysis that a recently developed technique called ankylography enables 3D image reconstruction using much fewer views than conventional tomography. Such a technique with the ability to obtain the 3D structure information from a few views is expected to find applications in both optical and x-ray imaging fields.

physics.optics↗
arXiv2013

What season suits you best? Seasonal light changes and cyanobacterial competition

Nearly all living organisms, including some bacterial species, exhibit biological processes with a period of about 24 h called circadian (from the Latin circa, about, dies, day) rhythms. These rhythms allow living organisms to anticipate the daily alternation of light and darkness. Experiments carried out in cyanobacteria have shown the adaptive value of circadian clocks. In these experiments a wild type cyanobacterial strain (with a 24 h circadian rhythm) and a mutant strain (with a longer or shorter period) grow in competition. In different experiments the external light dark cycle was changed in order to match the circadian period of the different strains, revealing that the strain whose circadian period matches the light-dark has a larger fitness. As a consequence the initial population of one strain grows while the other decays. These experiments were made under fixed light and dark intervals. However, in Nature this relationship changes according to the season. Therefore, seasonal changes in light could affect the results of the competition. Using a theoretical model we analyze how modulation of light can change the survival of the different cyanobacterial strains. Our results show that there is a clear shift in the competition due to the modulation of light, which could be verified experimentally.

q-bio.PE↗
arXiv2013

Experimental investigation of the trachea oscillation and its role in the pitch production

Several experiments have been performed to investigate the mechanical vibrations associated with trachea and larynx when Italian vowels are emitted. The mechanical measurements have been made by using two laser Doppler vibrometers (based on the well-known not-invasive optical measurement technique) coupled with the acoustic field measured by high-quality certified microphones. The recorded signals are analyzed by using well-established methods in time and frequency domains. The signals of the mechanical vibrations along the trachea and the larynx are compared with those of the acoustic ones. Focusing the attention of the signals' onsets, we can observe an upward propagation of the mechanical vibrations for which it is possible to estimate a delay between the traces. We observe that the mechanical oscillations at the trachea start before the larynx and acoustic oscillations. Moreover these tracheal oscillations are self-oscillations in time and are associated with the pitch production, indicating a further hydrodynamic instability at trachea. This leads to new insights in the mechanism controlling the pitch in the speech.

q-bio.TO↗
arXiv2013

Computational biology approach to uncover hepatitis C virus helicase operation

Hepatitis C virus helicase is a molecular motor that splits nucleic acid duplex structures during viral replication, therefore representing a promising target for antiviral treatment. Hence, a detailed understanding of the mechanism by which it operates would facilitate the development of efficient drug-assisted therapies aiming to inhibit helicase activity. Despite extensive investigations performed in the past, a thorough understanding of the activity of this important protein was lacking since the underlying internal conformational motions could not be resolved. Here we review investigations that have been previously performed by us for HCV helicase. Using methods of structure-based computational modelling it became possible to follow entire operation cycles of this motor protein in structurally resolved simulations and uncover the mechanism by which it moves along the nucleic acid and accomplishes strand separation. We also discuss observations from that study in the light of recent experimental studies that confirm our findings.

q-bio.BM↗
arXiv2013

Geometrical comparison of two protein structures using Wigner-D functions

In this paper, we develop a quantitative comparison method for two arbitrary protein structures. This method uses a root-mean-square deviation (RMSD) characterization and employs a series expansion of the protein's shape function in terms of the Wigner-D functions to define a new criterion, which is called a "similarity value". We further demonstrate that the expansion coefficients for the shape function obtained with the help of the Wigner-D functions correspond to structure factors. Our method addresses the common problem of comparing two proteins with different numbers of atoms. We illustrate it with a worked example.

physics.bio-ph↗
arXiv2013

On the ion-mediated interaction between protein and DNA

The mechanism allowing a protein to search of a target sequence on DNA is currently described as an intermittent process composed of 3D diffusion in bulk and 1D diffusion along the DNA molecule. Due to the relevant charge of protein and DNA, electrostatic interaction should play a crucial role during this search. In this paper, we explicitly derive the mean field theory allowing for a description of the protein-DNA electrostatics in solution. This approach leads to a unified model of the search process, where 1D and 3D diffusion appear as a natural consequence of the diffusion on an extended interaction energy profile.

physics.bio-ph↗
arXiv2013

Protein-DNA electrostatics: toward a new paradigm for protein sliding

Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any active process. It has been rapidly recognized that to achieve this task these proteins should be efficient at both searching (i.e. sampling fast relevant parts of DNA) and finding (i.e. recognizing the specific site). A two-mode search and variants of it have been suggested since the 70s to explain either a fast search or an efficient recognition. Combining these two properties at a phenomenological level is however more difficult as they appear to have antagonist roles. To overcome this difficulty, one may simply need to drop the dihcotomic view inherent to the two-mode search and look more thoroughly at the set of interactions between DNA-binding proteins and a given DNA segment either specific or non-specific. This chapter demonstrates that, in doing so in a very generic way, one may indeed find a potential reconciliation between a fast search and an efficient recognition. Although a lot remains to be done, this could be the time for a change of paradigm

physics.bio-ph↗
arXiv2013

Accuracy of translation on ribosome could be provided by a resonance of intramolecular oscillations in tRNA molecules

X-ray data indicate that complexes of ribosomes with cognate and near cognate tRNAs are very similar structurally, and this was the ground for a suggestion that the ribosome discriminates correct codon-anticodon pair because of its higher stability. Here an alternative explanation of kinetic proofreading is suggested, and intramolecular oscillations in tRNAs play a keystone role in it. Resonance of the oscillations allows the cognate codon-anticodon pair to be conserved due to fast energy transfer to other part of the tRNA molecule. This mechanism can potentially discriminate correct pair from an incorrect one even if they have similar stabilities.

physics.bio-ph↗
arXiv2013

The Foundations of Genodynamics: The Development of Metrics for Genomic-Environmental Interactions

Single nucleotide polymorphisms (SNPs) represent an important type of dynamic sites within the human genome. These common variants often locally correlate into more complex multi-SNP haploblocks that are maintained throughout generations in a stable population. The information encoded in the structure of common SNPs and SNP haploblock variation can be characterized through a normalized information content (NIC) metric. Such an intrinsic measure allows disparate regions of individual genomes and the genomes of various populations to be quantitatively compared in a meaningful way. Using our defined measures of genomic information, the interplay of maintained statistical variations due to the environmental baths within which stable populations exist can be interrogated. We develop the analogous "thermodynamics" characterizing the state variables for genomic populations that are stable under stochastic environmental stresses. Since living systems have not been found to develop in the absence of environmental influences, we focus on describing the analogous genomic free energy measures in this development. The intensive parameter describing how an environment drives genomic diversity is found to depend inversely upon the NIC of the genome of a stable population within that environment. Once this environmental potential has been determined from the whole genome of a population, additive state variables can be directly related to the probabilities of the occurrence of given viable SNP based units (alleles) within that genome. This formulation allows the determination of both population averaged state variables as well as the genomic energies of individual alleles and their combinations. The determination of individual allelic potentials then should allow the parameterization of specific environmental influences upon shared alleles across populations in varying environments.

q-bio.GN↗
arXiv2013

Evolutionary game theory and the tower of Babel of cooperation: Altruism, free-riding, parasitism and the structure of the interactions in a world with finite resources

The study of the evolution of cooperative behaviours --which provide benefits to others-- and altruism --which provides benefits to others at a cost to oneself-- has been on the core of the evolutionary game theoretical framework since its foundation. The fast development of the theory during the last years has improved our knowledge of the issue, but carried attached a diversification of concepts which affected communication between scientists. Furthermore, the main root of conflict in the struggle for life identified by Darwin, the limited amount of resources present in any ecosystem, which is assumed to keep a constant population size in most game theoretical studies, has only recently been taken into account as explicitly influencing the evolutionary process. This review concerns about both issues, the conceptual diversification during the last years and the new results of the resource dependent models. In extenso: After a historical introduction, a review of the most important concepts is carried out. Then it is shown that pairwise interactions and additive fitness determine prisoner's dilemmas (PDs) or harmony games, that two altruists interacting together may determine a PD, and that the interaction environment of the most cooperative and less selfish individual in any population is always a PD. After that, it is shown that in addition to altruists versus free-riders, the combination of free-riders and parasites determines a fundamentally different PD. Computer simulations are then carried out to show that random exploration of parasitism, free-riding and altruism enables coexistence of the three strategies without the need of reciprocating, punishing or rewarding strategies. To finish, the problem of the limitation of resources is reviewed, showing that...

q-bio.PE↗
arXiv2013

Towards slime mould colour sensor: Recognition of colours by Physarum polycephalum

Acellular slime mould Physarum polycephalum is a popular now user-friendly living substrate for designing of future and emergent sensing and computing devices. P. polycephalum exhibits regular patterns of oscillations of its surface electrical potential. The oscillation patterns are changed when the slime mould is subjected to mechanical, chemical, electrical or optical stimuli. We evaluate feasibility of slime-mould based colour sensors by illuminating Physarum with red, green, blue and white colours and analysing patterns of the slime mould's electrical potential oscillations. We define that the slime mould recognises a colour if it reacts to illumination with the colour by a unique changes in amplitude and periods of oscillatory activity. In laboratory experiments we found that the slime mould recognises red and blue colour. The slime mould does not differentiate between green and white colours. The slime mould also recognises when red colour is switched off. We also map colours to diversity of the oscillations: illumination with a white colour increases diversity of amplitudes and periods of oscillations, other colours studied increase diversity either of amplitude or period.

cs.ET↗
arXiv2013

Unfolding kinetics of periodic DNA hairpins

DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as function of the number of open base pairs and applied mechanical force. Using a commonly employed model, we first analyse for which types of sequences a particularly simple landscape structure is predicted, where forward and backward energy barriers between partly unfolded states are decreasing linearly with force. Stochastic unfolding trajectories for such molecules with simple FEL are subsequently generated by kinetic Monte Carlo simulations. Introducing probabilities that can be sampled from these trajectories, it is shown how the parameters characterising the FEL can be estimated. Already 300 trajectories, as typically generated in experiments, provide faithful results for the FEL parameters.

physics.bio-ph↗