Modern Biophysics Research Articles

Acoustic trapping in the undergraduate laboratory

Acoustic trapping is used in modern biophysics laboratories to study cell adhesion or aggregation, to sort particles, or to build model tissues. Here, we create an acoustic trapping setup in liquid for an undergraduate instructional laboratory that is low-cost, easy to build, and produces results in a 1-hour laboratory period. In this setup, we use a glass slide, cover slip, and double-sided tape to make the sample chamber. A piezo-electric transducer connected to a function generator serves as the acoustic source. We use this setup to measure the node spacing (millimeters) and the acoustic trap force (picoNewtons). We anticipate that the simplicity of the experimental setup, the tractability of the theoretical equations, and the richness of the research topics on the subject will lead to an undergraduate laboratory with many interesting student projects.

Protein structure prediction using the evolutionary algorithm USPEX.

Protein structure prediction is one of major problems of modern biophysics: current attempts to predict the tertiary protein structure from amino acid sequence are successful mostly when the use of big data and machine learning allows one to reduce the "prediction problem" to the "problem of recognition". Compared with recent successes of deep learning, classical predictive methods lag behind in their accuracy for the prediction of stable conformations. Therefore, in this work we extended the evolutionary algorithm USPEX to predict protein structure based on global optimization starting with the amino acid sequence. Moreover, we compared frequently used force fields for the task of protein structure prediction. Protein structure relaxation and energy calculations were performed using Tinker (with several different force fields) and Rosetta (with REF2015 force field) codes. To create new protein structure models in the USPEX algorithm, we developed novel variation operators. The test of the new method on seven proteins having (for simplicity) no cis-proline (with ω ≈ 0°) residues, and a length of up to 100 residues, revealed that our algorithm predicts tertiary structures of proteins with high accuracy. The comparison of the final potential energies of the predicted protein structures obtained using the USPEX and the Rosetta Abinitio approach showed that in most cases the developed algorithm found structures with close or even lower energy (Amber/Charmm/Oplsaal) and scoring function (REF2015). While USPEX has clearly demonstrated its ability to find very deep energy minima, our study showed that the existing force fields are not sufficiently accurate for accurate blind prediction of protein structures without further experimental verification.

The Weather Factory: Alan C. Burton and Military Research at the University of Western Ontario, 1945-70

This article examines the impact of military funding on the career of Dr Alan C. Burton (1904–79), who is widely remembered as a founding father of modern biophysics. Burton performed military research for the Canadian armed services during the earliest decades of the Cold War, securing funding and pursuing opportunities that advanced his career in medical science. Central to his military-sponsored research was a special climatic laboratory at the University of Western Ontario dubbed the Weather Factory, which enabled a long-running experimental research program on cold and the human body. Military sponsorship enabled the research that influenced Burton’s professional trajectory from mathematician and physicist to biologist, and thus played an important role in his development as a biophysicist and interdisciplinary health scientist in mid-century Canada.

The chemical Langevin equation for biochemical systems in dynamic environments.

Modeling and simulation of complex biochemical reaction networks form cornerstones of modern biophysics. Many of the approaches developed so far capture temporal fluctuations due to the inherent stochasticity of the biophysical processes, referred to as intrinsic noise. Stochastic fluctuations, however, predominantly stem from the interplay of the network with many other-and mostly unknown-fluctuating processes, as well as with various random signals arising from the extracellular world; these sources contribute extrinsic noise. Here, we provide a computational simulation method to probe the stochastic dynamics of biochemical systems subject to both intrinsic and extrinsic noise. We develop an extrinsic chemical Langevin equation (CLE)-a physically motivated extension of the CLE-to model intrinsically noisy reaction networks embedded in a stochastically fluctuating environment. The extrinsic CLE is a continuous approximation to the chemical master equation (CME) with time-varying propensities. In our approach, noise is incorporated at the level of the CME, and it can account for the full dynamics of the exogenous noise process, irrespective of timescales and their mismatches. We show that our method accurately captures the first two moments of the stationary probability density when compared with exact stochastic simulation methods while reducing the computational runtime by several orders of magnitude. Our approach provides a method that is practical, computationally efficient, and physically accurate to study systems that are simultaneously subject to a variety of noise sources.

Modern Biophysics Redefines Our Understanding of Fungal Cell Wall Structure, Complexity, and Dynamics.

ABSTRACTEven though the cell wall has been recognized as a crucial protective organelle for fungi, essential for its virulence and a unique emblem of this kingdom, biosynthesis of this organelle remains poorly understood. Our knowledge was based mainly in the past on the chemical analysis of cell wall mutants and on the biochemical study of a few synthases and transglycosidases. Recent developments in biophysical equipment and methods, such as solid-state nuclear magnetic resonance or cryo-electron microscopy, have promoted a better appreciation of the spatiotemporal dynamics of cell wall biosynthesis. The new information will be presented here with the cell wall of the human opportunistic pathogen Aspergillus fumigatus.

Conserved allosteric ensembles in disordered proteins using TROSY/anti-TROSY R2-filtered spectroscopy

Defining the role of intrinsic disorder in proteins in the myriad of biological processes with which it is involved represents a significant goal in modern biophysics. Toward this end, NMR is uniquely suited for molecular studies of dynamic and disordered regions, but studying these regions in concert with their more structured domains and binding partners presents spectroscopic challenges. Here, we investigate the interactions between the structured and disordered regions of the human glucocorticoid receptor (GR). To do this, we developed an NMR strategy that relies on a novel relaxation filter for the simultaneous study of structured and unstructured regions. Using this approach, we conducted a comparative analysis of three translational isoforms of GR containing a folded DNA-binding domain (DBD) and two disordered regions that flank the DBD, one of which varies in size in the different isoforms. Notably, we were able to assign resonances that had previously been inaccessible because of the spectral complexity of the translational isoforms, which in turn allowed us to 1) identify a region of the structured DBD that undergoes significant changes in the local chemical environment in the presence of the disordered region and 2) determine differences in the conformational ensembles of the disordered regions of the translational isoforms. Furthermore, an ensemble-based thermodynamic analysis of the isoforms reveals conserved patterns of stability within the N-terminal domain of GR that persist despite low sequence conservation. These studies provide an avenue for further investigations of the mechanistic underpinnings of the functional relevance of the translational isoforms of GR while also providing a general NMR strategy for studying systems containing both structured and disordered regions.

A Flexible Laboratory Exercise Introducing Practical Aspects of Mean Squared Displacement

ABSTRACT Mean squared displacement is a standard biophysical tool for characterizing the motion of particles in a thermally dominated environment, yet it is rarely formally introduced or discussed in undergraduate curriculum. Here, we provide a flexible and adaptable experimental or computational lab activity that provides a practical introduction to mean squared displacement and anomalous diffusion that includes optional experimental protocols and computational simulation techniques for data collection and discusses a variety of analysis techniques. This lab activity has been implemented both face-to-face and completely online and provides crucial experience in important research techniques, helping to bridge traditional undergraduate curriculum and modern biophysics research.

The VIth Congress of Biophysicists of Russia

An overview of the problems of modern biophysics, which were discussed at the VIth Congress of biophysicists of Russia, Sochi, September 2019 ( http://conf-2019.biophys.ru ), is given. The results of fundamental and applied research in the field of biophysics of single biomacromolecules and molecular complexes, membrane biophysics, cell biophysics, bionanotechnology were presented at the plenary, sectional, and poster sessions. Great attention was paid to issues on the application of information technology, mathematical and computer modeling, and bioinformatics methods as a necessary research tool at all levels of organization of living systems, from biomacromolecules to biogeocenoses, as well as to new experimental methods of biophysical research. Along with the fundamental problems of studying the physical mechanisms of the regulation of biological processes at the molecular, subcellular, and cellular levels, the application of biophysical research results in medicine and ecology was widely discussed. It was decided to hold the next Congress of biophysicists of Russia in 2023.

Генетико-математическое моделирование взаимодействия популяций, новая психонейроиммуноэндокринология и психонейроиммунология

Modern digital healthcare, biophysics and biology create new problems that stimulate the development of a new biophysical circuit and mathematical models from nuclear fusion (nuclear medicine) to genomic cell-organizational prognosis in neurophysiology, neuroendocrinology, psychoneuroimmunology and psychoneuroimmunoendocrinology. In this case, the following are effectively used: deterministic, stochastic, hybrid, multiscale modeling methods, as well as analytical and computational methods. The solution of a genetical-mathematical problem of interaction of cages of human population and virus population in relation to COVID-19 pandemic problem is submitted. A mathematical model based on the Hardy-Weinberg law is used, consisting of two interdependent differential equations. The equations reflect the temporal dynamics of the cells of human and viral populations during their interaction. Solutions of differential equations were found and the results of these solutions were analyzed. The pandemic duration is estimated using parameters of human liver cells and influenza virus. Perspective of further development of psychoneuroimmunology as interdisciplinary science, through algorithms and routing of digital health care, with expansion of psychoneurocommunications of professional interests in medicine, economics, sociology, cultural studies is shown. Modern neurobes and neuromarketing are built around Homo sapiens within a “reasonable environment” — a healthy individual space.

Efficient methods for determining folding free energies in single-molecule pulling experiments

The remarkable accuracy and versatility of single-molecule techniques make new measurements that are not feasible in bulk assays possible. Among these, the precise estimation of folding free energies using fluctuation theorems in nonequilibrium pulling experiments has become a benchmark in modern biophysics. In practice, the use of fluctuation relations to determine free energies requires a thorough evaluation of the usually large energetic contributions caused by the elastic deformation of the different elements of the experimental setup (such as the optical trap, the molecular linkers and the stretched-unfolded polymer). We review and describe how to optimally estimate such elastic energy contributions to extract folding free energies, using DNA and RNA hairpins as model systems pulled by laser optical tweezers. The methodology is generally applicable to other force-spectroscopy techniques and molecular systems.

Resident and progenitor stem cells of the heart: morphology and f unction properties and prospects for practical application

The analysis of literature data on one of the actual problem of modern cell biophysics and biotechnology dealing with mesenchimal stem cells and cordial progenitor cells taking part in reparation of myocardium after its injury and first of all after myocardial infarction was done. Biological properties and potential ability of these cells in reparation processes of myocardium are considered. The recent data on experiments using experimental animals and patients are given. The approaches to increase the efficacy of сell technologies in treatment of injured cardiomyocytes are discussed.

SIBPA on the crest of the Adriatic Sea wave: Introduction to the SIBPA XXIV (2018 congress) special issue

The Italian Society for Pure and Applied Biophysics (SIBPA) held its XXIV National Congress in the beautiful seaside town of Ancona, Italy, on September 10–13, 2018. This special issue features a selection of contributions from the Congress in all areas of modern biophysics including molecular, cellular, applied, computational and nanoscale biophysics. SIBPA pursues its institutional tasks and carries on its successful promotion of biophysical disciplines at the national and international levels, also trough the consolidation of its partnership with Biophysical Chemistry and Elsevier.

Eugene I. Rabinowitch: A prophet of photosynthesis and of peace in the world.

More than 45years have passed since Eugene I. Rabinowitch died, on May 15, 1973, at the age of 75, but many still remember him as a photosynthesis giant, the author of a 2000-page "Bible" on photosynthesis, a great chemist and physicist, a discoverer of several basic photoreactions, one of the founders of modern biophysics, a peacemaker, a poet, an architect, an artist, a wonderful human being, and above all a great mentor. Sir John Rotblatt cited Eugene Rabinowitch, together with Bertrand Russell, for their key contributions that led to the Nobel Peace Prize awarded in 1995 jointly to Rotblatt and the Pugwash Conferences on Science and World Affairs "for their efforts to diminish the part played by nuclear arms in international politics and, in the longer run, to eliminate such arms." Already in 1965, Eugene Rabinowitch had received the prestigious Kalinga Prize from UNESCO "in recognition of his work to encourage international cooperation among scientists and to bring to light the potential dangers of science to the public."

The Effect of Environmental Electromagnetic Radiation on Associate Formation in Aqueous Solutions

Abstract—We present the results of studies of the nature of the features known in modern biophysics in the manifestation of the associative properties of aqueous solutions of biologically active substances. The phenomena observed during associate formation can be related with the effect of microwaves, primarily, of ionospheric origin. We take the results into account of earlier quantitative quantum mechanical analysis of the physical mechanism of formation of cluster associates in a liquid aqueous medium with the participation of water molecules, due to their high affinity for the proton. Comparison of the developed ideas and the experiments on electromagnetic shielding of biological solutions diluted to various degrees confirms the reality of the proposed relation of the phenomena in biological media with microwave radiation.

Процеси утворення позитивних іонів при взаємодії електронів з молекулами тиміну

The work is aimed to solve the key problems of modern biophysics related to the study of fundamental mechanisms of interaction of ionizing radiation on living cells and stability of biological systems to its influence. The obtained data and their generalizations create a basis for understanding the interaction mechanisms and stability of biological systems to its influence. Investigation is aimed on the obtaining the new priority data about the characteristics of the life important biological molecules, establishing the mechanisms and features of dissociative capture, excitation and ionization under the slow electrons; the study of the influence of intermolecular interactions on these processes and solution of some applications concerning the definition of physical stability of biomolecules in different states of aggregation. The AM1 method that was used in research is a semi-empirical method for the quantum calculation of molecular electronic structure in computational chemistry. It is based on the neglect of differential diatomic overlap integral approximation and investigates the processes of formation of positive ions, which are formed during the interaction of thymine molecules with slow electrons. Fragmentation model of thymine molecules under electron ipmpact is proposed. Six most likely bond breaks in the cyclic structure of thymine molecular ion are identified. The obtained results are in good agreement with experimental data.

Multiscale Kinetic Modeling of a Cl−/H+ Antiporter: Integrating Simulation and Experiment to Characterize A Complex Ion Exchange Process

One of the central challenges in modern biophysics is understanding the molecular nature, and hence both the thermodynamics and kinetics, of coupled biomolecular transport mechanisms. The coupled ion exchange mechanism in Cl-/H+ antiporters offers an important and intriguing case study for this challenge. Herein, our new approach to multiscale kinetic modeling (MKM) and its application to characterize the Cl-/H+ exchange process in ClC-ec1 will be presented. We first calculate essential state-to-state rate coefficients with reactive and polarizable molecular dynamics simulations. A kinetic (Markov state) model is then used to optimize the rate coefficients within their calculated error to reproduce specific experimental rates and stoichiometry. This results in a set of solutions that not only predicts new, testable properties (e.g., rates at different pH values and the relative contribution of protein orientations), but also reveals insight into the series of transitions, the balance of rate-limiting steps, the molecular origin of the 2.2:1 Cl−/H+ stoichiometry, and the influence of protein orientation. Our results suggest that the consistent exchange ratio is a consequence of kinetic coupling wherein residue E148 plays an essential role through protonation-dependent anion transport, and an anion-dependent pKa value. They further demonstrate that a large conformational change is not essential at this level of modeling for the ion exchange mechanism, suggesting a more facile possible evolutionary connection to chloride channels. Finally, the results demonstrate how an ensemble of different exchange pathways, as opposed to a single series of transitions, culminates in the macroscopic observables and thereby explains the molecular mechanism.

Basic principles of confocal microscopy of cаlcium signals

Background: The study of fast processes occurring in living cells, for example, the dynamics of calcium ions or other ions, is actual for modern biophysics, physiology and medicine and can be carried out by laser scanning confocal microscopy. Confocal microscopy as a method of studying biological objects has a number of features requiring an understanding of the delicate mechanisms underlying it. Objectives: The aim of the work is the description of principles and details of measurements of calcium signals in the living cells using laser scanning confocal microscopy and fluorescent indicators. Materials and methods: The analysis of the methodological and practical aspects of studies of calcium signals was carried out by confocal microscopy in the work. Results: Confocal microscopy allows to study the changes in the concentration of free calcium within the cell and even a small part of it by a fluorescent dye, which increases the contrast in comparison with conventional fluorescence microscopy through an additional confocal aperture located in the front of the detector and the use of laser light source and scanning the object. To register calcium signals it is necessary to make a selection of a number of adequate parameters: the registration frequency, the size of a single scanning element (pixel), the sensitivity of the detector, the intensity of laser irradiation, the diameter of the confocal gap, the corresponding filters for exciting and emitting the fluorescent dye used and the corresponding dichroic mirror. An important stage of a setup of a confocal system is the determination of the value of the scattering function of a point. Compensation of the process of bleaching of the fluorescence dye and reduction of phototoxicity, minimization of the scattering process of the image allow to increase a reproducibility of the experiments. Conclusions: Using modern laser scanning confocal microscopes for registration of calcium signals from a small group of channels (for example, rianodine receptors) or the cell part, it is necessary to carefully select the parameters of the hardware setup, which are determined by the nature of the object of study and the peculiarities of the experimental conditions. This will allow to receive the reliable information about the functioning of both individual channels and the mechanisms of Ca2+ signaling of the whole cell or its part.

Asymptotic Approximation of the Stationary Solution with Internal Layer for FitzHugh–Nagumo System

Creating adequate mathematical models of processes in living nature is an important task of modern biophysics. Blood clotting, nerve impulse propagation, reduction of the heart muscle, the pattern-formation in nature are auto-wave processes. FitzHugh–Nagumo system of equations is used to describe the auto-wave processes in active media. Such math problems are usually solved by numerical methods. The use of resource-intensive algorithms is required in the case of auto-wave solutions with sharp gradients. Therefore, it is appropriate to use the analytical methods for this type of problems. In this paper, the asymptotic method of contrast structures theory is used to obtain an approximate solution of a singularly perturbed system of FitzHugh–Nagumo type. The method allows to reduce the non-linear system of equations to a number of problems that can be solved analytically or with a stable numerical algorithm. This study presents the asymptotic approximation of a stationary auto-wave solution of the considered system. Additionally, this paper provides a formula that specifies the location of internal transition layers. The results were compared with the numerical solution. The application of contrast structures theory to the study of active media models can be used for analytical studies of other such systems, improving existing models and increasing the efficiency of the numerical calculations.

Localized surface plasmon resonance in Au nanoprisms on glass substrates

Metal nanocrystals are actual objects for the modern biophysics mainly because of their usage in sensors based on localized surface plasmon resonance (LSPR) and as active substrates for surface-enhanced spectroscopies. This work deals with the experimental and theoretical investigation of optical properties of trigonal and hexagonal Au nanoprisms deposited on the glass substrates. It was confirmed for the studied structures that the LSPR spectra depend on the crystals shape and size. Theoretical modeling the optical properties of plasmon-supporting nanoprisms was performed using the finite-difference time-domain method. The experimentally obtained and theoretically modeled LSPR spectral positions were found to be different, which can be attributed to a high spread of nanoprism shapes and sizes in the same sample and to nanocrystals aggregation effect confirmed by microscopy data. Additionally, the distributions of the electric field in the vicinity of nanoprisms under the LSPR conditions were simulated, and a strong field intensity enhancement at the corners of the prisms was demonstrated, which implies the promising application of such plasmonic nanostructures for surface- enhanced spectroscopy.

An Original Theory Regarding the Correlations between the Extremely High Frequency Electromagnetic Waves of Athermic Intensities and their Cellular Effects

Lately it has been demonstrated that extremely low intensity millimeter therapy could represent an important new technological method, universal and effective in the treatment of diseases with various etiologies. In this way, millimeter waves have crystallized into a new branch of modern biophysics and cellular studies and are used extensively in medicine and biotechnology. Thus, in the present report, we will try to describe a new original theory regarding the interaction mechanism between extremely high frequency electromagnetic waves and their biological environment. This could be quite important since so far there has not been developed a general theory on the relations between extremely high frequency/extremely low intensity electromagnetic waves and the biological environment, at various levels of organization: submolecular, molecular, cellular, the organ level or the entire organism. In this way, the present paper was designed to contribute to the development and understanding of millimeter wave’s interaction with the biological entities and to propose a new alternative biophysical and cellular mechanism to explain the biological effects inherent to the electromagnetic millimeter field.