{"results":[{"id":"crossref_10.1051/bioconf/202622504001","title":"The impact of early termination of coal-fired power plant on achieving SDG#7 in Java Island-Indonesia","authors":[{"name":"Suksmo Satriyo Pangarso"},{"name":"Jaka Aminata"},{"name":"Nugroho Sumarjiyanto BM"}],"abstract":"Indonesia has 9 indicators of achieving Sustainable Development Goals (SDG) #7 at the national level. This study proposes the addition indicators for SDG#7 achievement to assess the readiness of provinces in Java Island in terms of ensuring access to affordable, sustainable, clean, and modern energy from electricity which associated with the early termination program of coal-fired power plant (CFPP). The additional indicators are access to electricity, reliability of electricity, electricity security and energy poverty. The results of this study indicate that based on the above-mentioned criteria, the program will have significant impact on the criteria of access to electricity and energy poverty.","source":"CrossRef","year":2026,"language":"en","subjects":null,"doi":"10.1051/bioconf/202622504001","url":"https://doi.org/10.1051/bioconf/202622504001","is_open_access":true,"published_at":"","score":70},{"id":"crossref_10.1021/acsabm.5c02324","title":"Mg-Hydroxyapatite Nanorods for Dual Intracellular Doxorubicin Delivery and Osteogenic-Associated BM-MSC Responses","authors":[{"name":"Federico Pupilli"},{"name":"Giada Bassi"},{"name":"Marta Tavoni"},{"name":"Monica Montesi"},{"name":"Anna Tampieri"},{"name":"Simone Sprio"}],"abstract":"","source":"CrossRef","year":2026,"language":"en","subjects":null,"doi":"10.1021/acsabm.5c02324","url":"https://doi.org/10.1021/acsabm.5c02324","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acsabm.5c02324","is_open_access":true,"published_at":"","score":70},{"id":"crossref_10.3390/w17172539","title":"Hydrogeochemical Characterization of Mineral Springs in Peruvian Tropical Highlands","authors":[{"name":"Damaris Leiva-Tafur"},{"name":"Hardy Geoffrey Manco Perez"},{"name":"Jesús Rascón"},{"name":"Lorenzo Culqui"},{"name":"Oscar Andrés Gamarra-Torres"},{"name":"Manuel Oliva-Cruz"}],"abstract":"Water quality in natural mineral springs is essential for sustainable use and conservation in the Amazon region. This study presents a hydrogeochemical characterization of 21 springs in the Peruvian Tropical Highlands, expanding on previous records of only six sources. The springs, which are thermal, saline, and sulfurous, are located between 384 and 3147 m a.s.l., mainly in mountainous areas with structural slopes and permeable sedimentary formations, such as the Pulluicana Group (composed mainly of sandstones and shales) and the Sarayaquillo Formation (characterized by reddish sandstones and siltstones). Physicochemical analysis showed temperatures ranging from 15.1 to 38.2 °C, pH from 5.20 to 8.72, conductivity between 0.05 and 253 mS/cm, and total dissolved solids from 0.02 to 162.50 g/L. High levels of arsenic and aluminum, likely originating from the natural weathering of rocks rich in these elements, exceeded national limits. Microbiological analysis detected fecal coliforms and Escherichia coli, indicating potential health risks. The results highlight the importance of regular monitoring and proper management to ensure safe use and explore its therapeutic and biotechnological applications, such as microbial bioremediation or development of extremophile-based enzymes.","source":"CrossRef","year":2025,"language":"en","subjects":null,"doi":"10.3390/w17172539","url":"https://doi.org/10.3390/w17172539","is_open_access":true,"published_at":"","score":69},{"id":"arxiv_2401.05208","title":"Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs. cgDNA+","authors":[{"name":"Wout Laeremans"},{"name":"Midas Segers"},{"name":"Aderik Voorspoels"},{"name":"Enrico Carlon"},{"name":"Jef Hooyberghs"}],"abstract":"Coarse-grained models have emerged as valuable tools to simulate long DNA molecules while maintaining computational efficiency. These models aim at preserving interactions among coarse-grained variables in a manner that mirrors the underlying atomistic description. We explore here a method for testing coarse-grained vs. all-atom models using stiffness matrices in Fourier space ($q$-stiffnesses), which are particularly suited to probe DNA elasticity at different length scales. We focus on a class of coarse-grained rigid base DNA models known as cgDNA and its most recent version cgDNA+. Our analysis shows that while cgDNA+ follows closely the $q$-stiffnesses of the all-atom model, the original cgDNA shows some deviations for twist and bending variables which are rather strong in the $q \\to 0$ (long length scale) limit. The consequence is that while both cgDNA and cgDNA+ give a suitable description of local elastic behavior, the former misses some effects which manifest themselves at longer length scales. In particular, cgDNA performs poorly on the twist stiffness with a value much lower than expected for long DNA molecules. Conversely, the all-atom and cgDNA+ twist is strongly length scale dependent: DNA is torsionally soft at a few base pair distances, but becomes more rigid at distances of a few dozens base pairs. Our analysis shows that the bending persistence length in all-atom and cgDNA+ is somewhat overestimated.","source":"arXiv","year":2024,"language":"en","subjects":["cond-mat.soft","cond-mat.stat-mech","q-bio.BM"],"doi":"10.1063/5.0197053","url":"https://arxiv.org/abs/2401.05208","pdf_url":"https://arxiv.org/pdf/2401.05208","is_open_access":true,"published_at":"2024-01-10T15:12:28Z","score":68},{"id":"arxiv_2409.16298","title":"BetterBodies: Reinforcement Learning guided Diffusion for Antibody Sequence Design","authors":[{"name":"Yannick Vogt"},{"name":"Mehdi Naouar"},{"name":"Maria Kalweit"},{"name":"Christoph Cornelius Miething"},{"name":"Justus Duyster"},{"name":"Joschka Boedecker"},{"name":"Gabriel Kalweit"}],"abstract":"Antibodies offer great potential for the treatment of various diseases. However, the discovery of therapeutic antibodies through traditional wet lab methods is expensive and time-consuming. The use of generative models in designing antibodies therefore holds great promise, as it can reduce the time and resources required. Recently, the class of diffusion models has gained considerable traction for their ability to synthesize diverse and high-quality samples. In their basic form, however, they lack mechanisms to optimize for specific properties, such as binding affinity to an antigen. In contrast, the class of offline Reinforcement Learning (RL) methods has demonstrated strong performance in navigating large search spaces, including scenarios where frequent real-world interaction, such as interaction with a wet lab, is impractical. Our novel method, BetterBodies, which combines Variational Autoencoders (VAEs) with RL guided latent diffusion, is able to generate novel sets of antibody CDRH3 sequences from different data distributions. Using the Absolut! simulator, we demonstrate the improved affinity of our novel sequences to the SARS-CoV spike receptor-binding domain. Furthermore, we reflect biophysical properties in the VAE latent space using a contrastive loss and add a novel Q-function based filtering to enhance the affinity of generated sequences. In conclusion, methods such as ours have the potential to have great implications for real-world biological sequence design, where the generation of novel high-affinity binders is a cost-intensive endeavor.","source":"arXiv","year":2024,"language":"en","subjects":["q-bio.BM","cs.LG"],"url":"https://arxiv.org/abs/2409.16298","pdf_url":"https://arxiv.org/pdf/2409.16298","is_open_access":true,"published_at":"2024-09-09T13:06:01Z","score":68},{"id":"arxiv_2307.15073","title":"Drug Discovery under Covariate Shift with Domain-Informed Prior Distributions over Functions","authors":[{"name":"Leo Klarner"},{"name":"Tim G. J. Rudner"},{"name":"Michael Reutlinger"},{"name":"Torsten Schindler"},{"name":"Garrett M. Morris"},{"name":"Charlotte Deane"},{"name":"Yee Whye Teh"}],"abstract":"Accelerating the discovery of novel and more effective therapeutics is an important pharmaceutical problem in which deep learning is playing an increasingly significant role. However, real-world drug discovery tasks are often characterized by a scarcity of labeled data and significant covariate shift$\\unicode{x2013}\\unicode{x2013}$a setting that poses a challenge to standard deep learning methods. In this paper, we present Q-SAVI, a probabilistic model able to address these challenges by encoding explicit prior knowledge of the data-generating process into a prior distribution over functions, presenting researchers with a transparent and probabilistically principled way to encode data-driven modeling preferences. Building on a novel, gold-standard bioactivity dataset that facilitates a meaningful comparison of models in an extrapolative regime, we explore different approaches to induce data shift and construct a challenging evaluation setup. We then demonstrate that using Q-SAVI to integrate contextualized prior knowledge of drug-like chemical space into the modeling process affords substantial gains in predictive accuracy and calibration, outperforming a broad range of state-of-the-art self-supervised pre-training and domain adaptation techniques.","source":"arXiv","year":2023,"language":"en","subjects":["q-bio.BM","cs.LG","stat.ML"],"url":"https://arxiv.org/abs/2307.15073","pdf_url":"https://arxiv.org/pdf/2307.15073","is_open_access":true,"published_at":"2023-07-14T05:01:10Z","score":67},{"id":"crossref_10.15294/biosaintifika.v15i3.41987","title":"The application of Rigidoporus sp J12 and Stenotrophomonas maltophilia BM in the degradation of batik waste","authors":[{"name":"Yohanes Subowo"},{"name":"Suliasih Suliasih"},{"name":"Sri Widawati"}],"abstract":"The batik industry in Indonesia produces batik waste which pollutes the environment. This waste can be degraded using laccase-producing microorganisms. The microorganisms used in the research were the fungus Rigidoporus sp J12 and the bacteria Stenotrophomonas maltophilia BM. This research aims to determine the ability of Rigidoporus sp J12 and Stenotrophomonas maltophilia BM and their consortium in producing laccase, observing their ability to degrade Poly R-478 which is an indicator of phenoloxidase activity and batik waste. Microorganisms are grown in growth media and then placed in media containing Poly R-478 or batik waste. Inducers are added to increase laccase activity. The inducers used were 15 g/L sucrose, 200 µM CuSO4 and 40 mM veratryl alcohol. The results showed that Rigidoporus sp J12 and Stenotrophomonas maltophilia BM produced laccase in PDB and NA media. The highest laccase activity was found in the enzyme produced by Rigidoporus sp J12 in PDB media at a temperature of 40°C, media pH 6.0 and the addition of sucrose. Rigidoporus sp J12 degraded batik waste by 39.38% and increased by 2.12 times after adding sucrose and incubation for 15 days. These bacteria and fungi can be used to degrade batik waste in order to prevent environmental pollution. Using the fungus Rigidoporus sp J12 purely is more profitable than using it with S. maltophilia BM bacteria.","source":"CrossRef","year":2023,"language":"en","subjects":null,"doi":"10.15294/biosaintifika.v15i3.41987","url":"https://doi.org/10.15294/biosaintifika.v15i3.41987","pdf_url":"https://journal.unnes.ac.id/nju/index.php/biosaintifika/article/viewFile/41987/15322","is_open_access":true,"published_at":"","score":67},{"id":"arxiv_2203.04671","title":"A preparative mass spectrometer to deposit intact large native protein complexes","authors":[{"name":"Paul Fremdling"},{"name":"Tim K. Esser"},{"name":"Bodhisattwa Saha"},{"name":"Alexander Makarov"},{"name":"Kyle Fort"},{"name":"Maria Reinhardt-Szyba"},{"name":"Joseph Gault"},{"name":"Stephan Rauschenbach"}],"abstract":"Electrospray ion-beam deposition (ES-IBD) is a versatile tool to study structure and reactivity of molecules from small metal clusters to large protein assemblies. It brings molecules gently into the gas phase where they can be accurately manipulated and purified, followed by controlled deposition onto various substrates. In combination with imaging techniques, direct structural information of well-defined molecules can be obtained, which is essential to test and interpret results from indirect mass spectrometry techniques. To date, ion-beam deposition experiments are limited to a small number of custom instruments worldwide, and there are no commercial alternatives. Here we present a module that adds ion-beam deposition capabilities to a popular commercial MS platform (Thermo Scientific$^{\\mathrm{TM}}$ Q Exactive$^{\\mathrm{TM}}$ UHMR). This combination significantly reduces the overhead associated with custom instruments, while benefiting from established high performance and reliability. We present current performance characteristics including beam intensity, landing-energy control, and deposition spot size for a broad range of molecules. In combination with atomic force microscopy (AFM) and transmission electron microscopy (TEM), we distinguish near-native from unfolded proteins and show retention of native shape of protein assemblies after dehydration and deposition. Further, we use an enzymatic assay to quantify activity of an non-covalent protein complex after deposition an a dry surface. Together, these results indicate a great potential of ES-IBD for applications in structural biology, but also outline the challenges that need to be solved for it to reach its full potential.","source":"arXiv","year":2022,"language":"en","subjects":["q-bio.BM"],"doi":"10.1021/acsnano.2c04831","url":"https://arxiv.org/abs/2203.04671","pdf_url":"https://arxiv.org/pdf/2203.04671","is_open_access":true,"published_at":"2022-03-09T12:24:23Z","score":66},{"id":"arxiv_2011.03442","title":"DeepFoldit -- A Deep Reinforcement Learning Neural Network Folding Proteins","authors":[{"name":"Dimitra N. Panou"},{"name":"Martin Reczko"}],"abstract":"Despite considerable progress, ab initio protein structure prediction remains suboptimal. A crowdsourcing approach is the online puzzle video game Foldit, that provided several useful results that matched or even outperformed algorithmically computed solutions. Using Foldit, the WeFold crowd had several successful participations in the Critical Assessment of Techniques for Protein Structure Prediction. Based on the recent Foldit standalone version, we trained a deep reinforcement neural network called DeepFoldit to improve the score assigned to an unfolded protein, using the Q-learning method with experience replay. This paper is focused on model improvement through hyperparameter tuning. We examined various implementations by examining different model architectures and changing hyperparameter values to improve the accuracy of the model. The new model hyper-parameters also improved its ability to generalize. Initial results, from the latest implementation, show that given a set of small unfolded training proteins, DeepFoldit learns action sequences that improve the score both on the training set and on novel test proteins. Our approach combines the intuitive user interface of Foldit with the efficiency of deep reinforcement learning.","source":"arXiv","year":2020,"language":"en","subjects":["q-bio.BM","cs.LG"],"url":"https://arxiv.org/abs/2011.03442","pdf_url":"https://arxiv.org/pdf/2011.03442","is_open_access":true,"published_at":"2020-10-28T16:05:42Z","score":64},{"id":"arxiv_1805.01735","title":"Optimizing Native Ion Mobility Q-TOF in Helium and Nitrogen for Very Fragile Noncovalent Interactions","authors":[{"name":"Valérie Gabelica"},{"name":"Sandrine Livet"},{"name":"Frédéric Rosu"}],"abstract":"The meaningful comparison of ion mobility (IM) results and of collision cross section (CCS) values on different platforms is a prerequisite for using CCS for identification or structural assignment. The amount of internal energy imparted to the ions prior to the ion mobility cell is a source of experimental variation. Here we investigated the effects of virtually all tuning parameters of the Agilent 6560 IM-Q-TOF on the arrival time distributions of Ubiquitin7+, and found conditions in which the native state prevails. We will discuss the effects of solvent evaporation conditions in the source, in the entire pre-IM DC voltage gradient, and with the funnel RF amplitudes, and will also report on ubiquitin7+ conformations in different solvents, including native supercharging conditions. Collision-induced unfolding (CIU) can be conveniently provoked in two distinct regions: behind the source capillary (by changing the fragmentor voltage) and in the trapping funnel (by changing the trap entrance grid delta voltage). The softness of the instrumental conditions were then optimized with the benchmark DNA G-quadruplex [(dG4T4G4)2.(NH4+)3-8H]5-, for which ion activation results in ammonia loss. To reduce the ion internal energy and obtain the intact 3-NH4+ complex, we reduced the post-IM voltage gradient, but this resulted in a lower IM resolving power due to increased diffusion behind the drift tube. The article thus describes the various trade-offs between ion activation, ion transmission, and ion mobility performance for native MS of very fragile structures.","source":"arXiv","year":2018,"language":"en","subjects":["q-bio.QM","q-bio.BM"],"doi":"10.1007/s13361-018-2029-4","url":"https://arxiv.org/abs/1805.01735","pdf_url":"https://arxiv.org/pdf/1805.01735","is_open_access":true,"published_at":"2018-05-04T12:15:42Z","score":62},{"id":"crossref_10.1007/s11626-015-9995-7","title":"BM-MSCs and Bio-Oss complexes enhanced new bone formation during maxillary sinus floor augmentation by promoting differentiation of BM-MSCs","authors":[{"name":"Qian Zhou"},{"name":"Bo-Han Yu"},{"name":"Wei-Cai Liu"},{"name":"Zuo-Lin Wang"}],"abstract":"","source":"CrossRef","year":2016,"language":"en","subjects":null,"doi":"10.1007/s11626-015-9995-7","url":"https://doi.org/10.1007/s11626-015-9995-7","pdf_url":"http://link.springer.com/content/pdf/10.1007/s11626-015-9995-7.pdf","is_open_access":true,"citations":10,"published_at":"","score":60.3},{"id":"arxiv_1607.07809","title":"Entropic formulation for the protein folding process: hydrophobic stability correlates with folding rates","authors":[{"name":"J. P. Dal Molin"},{"name":"A. Caliri"}],"abstract":"We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our main tool of investigation is a 3D lattice model provided with a ten-letter alphabet, the stereochemical model. This model was conceived for Monte Carlo (MC) simulations when one keeps in mind the kinetic behavior of protein-like chains in solution. In order to characterize the folding characteristic time (τ) by two distinct sampling methods, first we present two sets of 10^{3} MC simulations for a fast protein-like sequence. For these sets of folding times, τ and τ_{q} were obtained with the application of the standard Metropolis algorithm (MA), and a modified algorithm (M_{q}A). The results for τ_{q}reveal two things: i) the hydrophobic chain-solvent interactions plus a set of inter-residues steric constraints are enough to emulate the first stage of the process: for each one of the 10^{3} MC performed simulations, the native is always found without exception, ii) the ratio τ_{q}/τ~1/3 suggests that the effect of local thermal fluctuations, encompassed by the Tsallis weight, provides an innate efficiency to the chain escapes from energetic and steric traps. ...","source":"arXiv","year":2016,"language":"en","subjects":["physics.bio-ph","cond-mat.soft","q-bio.BM"],"url":"https://arxiv.org/abs/1607.07809","pdf_url":"https://arxiv.org/pdf/1607.07809","is_open_access":true,"published_at":"2016-07-26T17:11:11Z","score":60},{"id":"arxiv_1307.6801","title":"Energy landscape theory for cotranslational protein folding","authors":[{"name":"David S. Tourigny"}],"abstract":"Energy landscape theory describes how a full-length protein can attain its native fold after sampling only a tiny fraction of all possible structures. Although protein folding is now understood to be concomitant with synthesis on the ribosome there have been few attempts to modify energy landscape theory by accounting for cotranslational folding. This paper introduces a model for cotranslational folding that leads to a natural definition of a nested energy landscape. By applying concepts drawn from submanifold differential geometry the dynamics of protein folding on the ribosome can be explored in a quantitative manner and conditions on the nested potential energy landscapes for a good cotranslational folder are obtained. A generalisation of diffusion rate theory using van Kampen's technique of composite stochastic processes is then used to account for entropic contributions and the effects of variable translation rates on cotranslational folding. This stochastic approach agrees well with experimental results and Hamiltionian formalism in the deterministic limit.","source":"arXiv","year":2013,"language":"en","subjects":["q-bio.BM","physics.bio-ph"],"url":"https://arxiv.org/abs/1307.6801","pdf_url":"https://arxiv.org/pdf/1307.6801","is_open_access":true,"published_at":"2013-07-25T15:53:50Z","score":57},{"id":"arxiv_1111.2323","title":"A Statistical Mechanical Approach to Protein Aggregation","authors":[{"name":"John S. Schreck"},{"name":"Jian-Min Yuan"}],"abstract":"We develop a theory of aggregation using statistical mechanical methods. An example of a complicated aggregation system with several levels of structures is peptide/protein self-assembly. The problem of protein aggregation is important for the understanding and treatment of neurodegenerative diseases and also for the development of bio-macromolecules as new materials. We write the effective Hamiltonian in terms of interaction energies between protein monomers, protein and solvent, as well as between protein filaments. The grand partition function can be expressed in terms of a Zimm-Bragg-like transfer matrix, which is calculated exactly and all thermodynamic properties can be obtained. We start with two-state and three-state descriptions of protein monomers using Potts models that can be generalized to include q-states, for which the exactly solvable feature of the model remains. We focus on n X N lattice systems, corresponding to the ordered structures observed in some real fibrils. We have obtained results on nucleation processes and phase diagrams, in which a protein property such as the sheet content of aggregates is expressed as a function of the number of proteins on the lattice and inter-protein or interfacial interaction energies. We have applied our methods to Aβ(1-40) and Curli fibrils and obtained results in good agreement with experiments.","source":"arXiv","year":2011,"language":"en","subjects":["q-bio.BM"],"doi":"10.1016/j.bpj.2011.11.1400","url":"https://arxiv.org/abs/1111.2323","pdf_url":"https://arxiv.org/pdf/1111.2323","is_open_access":true,"published_at":"2011-11-09T20:38:06Z","score":55},{"id":"arxiv_1009.3607","title":"Simple Model of the Transduction of Cell-Penetrating Peptides","authors":[{"name":"Kevin Cahill"}],"abstract":"Cell-penetrating peptides (CPPs) such as HIV's trans-activating transcriptional activator (TAT) and polyarginine rapidly pass through the plasma membranes of mammalian cells by an unknown mechanism called transduction. They may be medically useful when fused to well-chosen chains of fewer than about 35 amino acids. I offer a simple model of transduction in which phosphatidylserines and CPPs effectively form two plates of a capacitor with a voltage sufficient to cause the formation of transient pores (electroporation). The model is consistent with experimental data on the transduction of oligoarginine into mouse C2-C12 myoblasts and makes three testable predictions.","source":"arXiv","year":2010,"language":"en","subjects":["q-bio.BM"],"doi":"10.1049/iet-syb.2008.0160","url":"https://arxiv.org/abs/1009.3607","pdf_url":"https://arxiv.org/pdf/1009.3607","is_open_access":true,"published_at":"2010-09-19T04:34:30Z","score":54},{"id":"crossref_10.1016/s0992-5945(10)70565-1","title":"Controverse sur l’obligation d’avoir une DES-BM pour exercer à l’hôpital","authors":[{"name":"Valérie Lequien"}],"abstract":"","source":"CrossRef","year":2010,"language":"en","subjects":null,"doi":"10.1016/s0992-5945(10)70565-1","url":"https://doi.org/10.1016/s0992-5945(10)70565-1","is_open_access":true,"published_at":"","score":54},{"id":"arxiv_0910.4015","title":"Model for solvent viscosity effect on enzymatic reactions","authors":[{"name":"A. E. Sitnitsky"}],"abstract":"Why reaction rate constants for enzymatic reactions are typically inversely proportional to fractional power exponents of solvent viscosity remains to be already a thirty years old puzzle. Available interpretations of the phenomenon invoke to either a modification of 1. the conventional Kramers' theory or that of 2. the Stokes law. We show that there is an alternative interpretation of the phenomenon at which neither of these modifications is in fact indispensable. We reconcile 1. and 2. with the experimentally observable dependence. We assume that an enzyme solution in solvent with or without cosolvent molecules is an ensemble of samples with different values of the viscosity for the movement of the system along the reaction coordinate. We assume that this viscosity consists of the contribution with the weight $q$ from cosolvent molecules and that with the weight $1-q$ from protein matrix and solvent molecules. We introduce heterogeneity in our system with the help of a distribution over the weight $q$. We verify the obtained solution of the integral equation for the unknown function of the distribution by direct substitution. All parameters of the model are related to experimentally observable values. General formalism is exemplified by the analysis of literature experimental data for oxygen escape from hemerythin.","source":"arXiv","year":2009,"language":"en","subjects":["q-bio.BM"],"doi":"10.1016/j.chemphys.2010.02.005","url":"https://arxiv.org/abs/0910.4015","pdf_url":"https://arxiv.org/pdf/0910.4015","is_open_access":true,"published_at":"2009-10-21T08:24:50Z","score":53},{"id":"arxiv_0802.1056","title":"Genetic Code: Four-Codon and Non-Four-Codon Degeneracy","authors":[{"name":"Miloje M. Rakocevic"}],"abstract":"In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict distinction in Genetic Code Table (GCT) into some different quantums: 20, 23, 61 amino acid molecules. These molecules distinction is followed by specific balanced atom number and/or nucleon number distinctions within those molecules. In this second version two appendices are added; also a new version of Periodic system of numbers, whose first verson is given in arXiv:1107.1998 [q-bio.OT].","source":"arXiv","year":2008,"language":"en","subjects":["q-bio.BM","q-bio.GN"],"url":"https://arxiv.org/abs/0802.1056","pdf_url":"https://arxiv.org/pdf/0802.1056","is_open_access":true,"published_at":"2008-02-07T20:00:52Z","score":52},{"id":"arxiv_q-bio/0703011","title":"Genetic Code as a Harmonic System: three Supplements","authors":[{"name":"Miloje M. Rakocevic"}],"abstract":"The paper represents three supplements to the source paper, q-bio/0610044 [q-bio.OT], with three new series of harmonic structures of the genetic code, determined by Gauss arithmetical algorithm; by Table of Minimal Adding, as in (Rakocevic, 2011a: Table 4; 2011b: Table 4); all structures in relation to Binary-code tree (Rakocevic, 1998). The determination itself is realized through atom and nucleon number balancing and nuancing of molekular polarity. In the first supplement the word is about some additional harmonic structures in relation to a previous our paper (Rakocevic, 2004); in the second one about the relation that structures with the polarity of protein amino acids. In the third supplement we give new ideas about the genetic code by an inclusion of the notions cipher of the genetic code and the key of that cipher.","source":"arXiv","year":2007,"language":"en","subjects":["q-bio.OT","q-bio.BM"],"url":"https://arxiv.org/abs/q-bio/0703011","pdf_url":"https://arxiv.org/pdf/q-bio/0703011","is_open_access":true,"published_at":"2007-03-05T06:15:21Z","score":51},{"id":"arxiv_0706.3090","title":"Flexible-to-semiflexible chain crossover on the pressure-area isotherm of lipid bilayer","authors":[{"name":"I. N. Krivonos"},{"name":"S. I. Mukhin"}],"abstract":"We found theoretically that competition between ~Kq^4 and ~Qq^2 terms in the Fourier transformed conformational energy of a single lipid chain, in combination with inter-chain entropic repulsion in the hydrophobic part of the lipid (bi)layer, may cause a crossover on the bilayer pressure-area isotherm P(A)~(A-A_0)^{-n}. The crossover manifests itself in the transition from n=5/3 to n=3. Our microscopic model represents a single lipid molecule as a worm-like chain with finite irreducible cross-section area A_0, flexural rigidity K and stretching modulus Q in a parabolic potential with self-consistent curvature B(A) formed by entropic interactions between hydrocarbon chains in the lipid layer. The crossover area per lipid A* obeys relation Q^2/(KB(A*))~1 . We predict a peculiar possibility to deduce effective elastic moduli K and Q of the individual hydrocarbon chain from the analysis of the isotherm possessing such crossover. Also calculated is crossover-related behavior of the area compressibility modulus K_a, equilibrium area per lipid A_t, and chain order parameter S.","source":"arXiv","year":2007,"language":"en","subjects":["q-bio.QM","q-bio.BM"],"doi":"10.1007/s11447-008-1011-6","url":"https://arxiv.org/abs/0706.3090","pdf_url":"https://arxiv.org/pdf/0706.3090","is_open_access":true,"published_at":"2007-06-21T06:43:32Z","score":51}],"total":300980,"page":1,"page_size":20,"sources":["arXiv","CrossRef"],"query":"q-bio.BM"}