Extracting chemical energy by growing disorder: Efficiency at maximum power

We consider the efficiency of chemical energy extraction from the environment by the growth of a copolymer made of two constituent units in the entropy-driven regime. We show that the thermodynamic nonlinearity associated with the information processing aspect is responsible for a branching of the system properties such as power, speed of growth, entropy production, and efficiency, with varying affinity. The standard linear thermodynamics argument which predicts an efficiency of 1/2 at maximum power is inappropriate because the regime of maximum power is located either outside of the linear regime or on a separate bifurcated branch, and because the usual thermodynamic force is not the natural variable for this optimization.Comment: 6 pages, 4 figure

Solitons in the Yakushevich model of DNA beyond the contact approximation

The Yakushevich model of DNA torsion dynamics supports soliton solutions, which are supposed to be of special interest for DNA transcription. In the discussion of the model, one usually adopts the approximation $\ell_0 \to 0$, where $\ell_0$ is a parameter related to the equilibrium distance between bases in a Watson-Crick pair. Here we analyze the Yakushevich model without $\ell_0 \to 0$. The model still supports soliton solutions indexed by two winding numbers $(n,m)$; we discuss in detail the fundamental solitons, corresponding to winding numbers (1,0) and (0,1) respectively

Casimir-Polder interaction between an atom and a small magnetodielectric sphere

On the basis of macroscopic quantum electrodynamics and point-scattering techniques, we derive a closed expression for the Casimir-Polder force between a ground-state atom and a small magnetodielectric sphere in an arbitrary environment. In order to allow for the presence of both bodies and media, local-field corrections are taken into account. Our results are compared with the known van der Waals force between two ground-state atoms. To continuously interpolate between the two extreme cases of a single atom and a macroscopic sphere, we also derive the force between an atom and a sphere of variable radius that is embedded in an Onsager local-field cavity. Numerical examples illustrate the theory.Comment: 9 pages, 4 figures, minor addition

Mutagenesis-Mediated Virus Extinction: Virus-Dependent Effect of Viral Load on Sensitivity to Lethal Defection

Background: Lethal mutagenesis is a transition towards virus extinction mediated by enhanced mutation rates during viral genome replication, and it is currently under investigation as a potential new antiviral strategy. Viral load and virus fitness are known to influence virus extinction. Here we examine the effect or the multiplicity of infection (MOI) on progeny production of several RNA viruses under enhanced mutagenesis. Results: The effect of the mutagenic base analogue 5-fluorouracil (FU) on the replication of the arenavirus lymphocytic choriomeningitis virus (LCMV) can result either in inhibition of progeny production and virus extinction in infections carried out at low multiplicity of infection (MOI), or in a moderate titer decrease without extinction at high MOI. The effect of the MOI is similar for LCMV and vesicular stomatitis virus (VSV), but minimal or absent for the picornaviruses foot-and-mouth disease virus (FMDV) and encephalomyocarditis virus (EMCV). The increase in mutation frequency and Shannon entropy (mutant spectrum complexity) as a result of virus passage in the presence of FU was more accentuated at low MOI for LCMV and VSV, and at high MOI for FMDV and EMCV. We present an extension of the lethal defection model that agrees with the experimental results. Conclusions: (i) Low infecting load favoured the extinction of negative strand viruses, LCMV or VSV, with an increase of mutant spectrum complexity. (ii) This behaviour is not observed in RNA positive strand viruses, FMDV or EMCV. (iii) The accumulation of defector genomes may underlie the MOI-dependent behaviour. (iv) LCMV coinfections are allowed but superinfection is strongly restricted in BHK-21 cells. (v) The dissimilar effects of the MOI on the efficiency of mutagenic-based extinction of different RNA viruses can have implications for the design of antiviral protocols based on lethal mutagenesis, presently under development. © 2012 Moreno et al.Centro de Biología Molecular Severo Ochoa; Ministerio de Ciencia e Innovación (MICINN); Fundación Ramón ArecesPeer Reviewe

Bone-anchored titanium implants for auricular rehabilitation: case report and review of literature

CONTEXT AND OBJECTIVE: Osseointegrated implants have acquired an important role in the prosthetic rehabilitation of patients with craniofacial defects. The main indications are lack of local tissue for autogenous reconstruction, previous reconstruction failure and selection of this technique by the patient. This paper presents a clinical case and discusses indications and advantages of the osseointegrated implant technique for retention of auricular prostheses. TYPE OF STUDY: Case report, Universidade Federal de São Paulo (UNIFESP). METHODS: A female patient received three auricular implants after surgical resection of a hemangioma in her left ear. The time taken for osseointegration of the temporal bone was three months. After fabrication of the implant-retained auricular prosthesis, the patient was monitored for 12 months. RESULTS: The clinical parameters evaluated showed good postoperative healing, healthy peri-implant tissue, good hygiene and no loss of implants. Good hygiene combined with thin and immobile peri-implant soft tissues resulted in minimal complications. Craniofacial implant integration appears to be site-dependent; increasing age affects osseointegration in the temporal bone. The frequency of adverse skin reactions in peri-implant tissues is generally low. CONCLUSION: The surgical technique for rehabilitation using implant-retained auricular prostheses seems to be simple. It is associated with low rates of adverse skin reactions and long-term complications. Prostheses anchored by osseointegrated implants seem to provide better retention than do prostheses supported on spectacle frames, less risk of discoloration through the use of adhesives and better esthetic results than do prostheses anchored in the surgical cavityCONTEXTO E OBJETIVO: Os implantes osseointegrados adquiriram papel importante na reabilitação protética de pacientes com defeitos craniofaciais. As principais indicações são ausência local de tecidos para reconstrução autógena, falha anterior de reconstrução e opção do paciente. Este artigo apresenta um caso clínico e discute as indicações e vantagens da técnica de implantes osseointegrados para a retenção de próteses auriculares. TIPO DE ESTUDO E LOCAL: Relato de caso clínico, Universidade Federal de São Paulo (UNIFESP). MÉTODOS: Paciente do sexo feminino recebeu três implantes na região auricular após ressecção cirúrgica de hemangioma na orelha esquerda. O tempo de osseointegração no osso temporal foi de três meses. Após a confecção de prótese auricular implanto-suportada, a paciente foi observada por 12 meses. RESULTADOS: Os parâmetros clínicos analisados mostraram boa cicatrização pós-operatória, saúde dos tecidos adjacentes ao implante, boa higiene e nenhuma perda de implantes. A boa higiene combinada a pouca espessura e imobilidade dos tecidos moles perimplantares resulta em poucas complicações. A integração dos implantes craniofaciais parece variar conforme o local, e a idade avançada afeta a osseointegração no osso temporal. A frequência de reações adversas cutâneas nos tecidos perimplantares é geralmente baixa. CONCLUSÃO: A técnica cirúrgica para a reabilitação com próteses auriculares implanto-suportadas parece ser simples e está associada a baixos índices de reações cutâneas adversas e complicações no longo prazo. As próteses ancoradas por implantes osseointegrados parecem proporcionar melhor retenção do que as próteses suportadas nas armações de óculos, menor possibilidade de descoloração pelo uso de adesivos e melhores resultados estéticos do que as próteses ancoradas na cavidade cirúrgica.Universidade Federal de São Paulo (UNIFESP) Department of Otorhinolaryngology and Head and Neck SurgeryUniversidade Paulista Faculty of Dentistry Department of StomatologyUniversidade Federal de São Paulo (UNIFESP) Santo Amaro University School of DentistryUniversidade Federal de São Paulo (UNIFESP) Santo Amaro University Department of StomatologyUniversity of Gothenburg Department of Anatomy and Cell BiologyUniversity of Gothenburg Department of OtolaryngologyUNIFESP, Department of Otorhinolaryngology and Head and Neck SurgeryUNIFESP, Santo Amaro University School of DentistryUNIFESP, Santo Amaro University Department of StomatologySciEL

ELECTRONIC-CONFORMATIONAL INTERACTIONS IN PROTEINS

ABSTRACT The functionality of biopolymers and of the supermolecular structures in biology depends strongly on the interactions between electronic excitations and the shifts of the electronic density with the conformational changes in these systems. The study of the electronic-conformational interactions can help to form the physical theory of enzymatic activity and of the other biomolecular phenomena. The concept of the conformon can be introduced for the theoretical description of the electronic-conformational interactions, describing a kind of the quasi-particle containing the shift of the electronic density and the conformational changes. The direct experimental investigations of the electronic-conformational interactions were performed with the systems apo-aspartate-amino transferase with a series of different coenzymes

Energy and negentropy in enzymic catalysis

Abstract Sequence-specific conformational strains (SSCS) of biopolymers that carry free energy and genetic information have been called conformons, a term coined independently by two groups over two and a half decades ago [Green, D.E., Ji, S., 1972. The electromechanochemical model of mitochondrial structure and function. In: Schultz, J., Cameron, B. Sci. 227,[419][420][421][422][423][424][425][426][427][428][429][430][431][432][433][434][435][436][437]. To illustrate a practical application, the conformon theory was applied to the molecular-clamp model of DNA gyrase proposed by Berger and Wang [Berger, J.M., Wang, J.C., 1996. Recent developments in DNA topoisomerases II structure and mechanism. Curr. Opin. Struct. Biol. 6(1), 84-90], leading to the proposal of an eight-step molecular mechanism for the action of the enzyme. Finally, a set of experimentally testable predictions has been formulated on the basis of the conformon theory

Equilibrium and kinetic aspects of protein-DNA recognition.

The specificity of regulatory protein binding to DNA is due to a complementarity between the sequence of reaction centres on the protein and the base pair sequence in the specific DNA site allowing the formation of a number of specific noncovalent bonds between the interacting entities. In the present communication the thermodynamic and kinetic aspects of these interactions are considered. The extent of binding specificity is shown to increase with an increase of the bond stability constants and with an increase in the number of ligand reaction centres. Kinetic analysis is carried out assuming that association process is very fast and that dissociation of nonspecific complexes is a rate-limiting step in the recognition of a specific binding site on DNA. The calculations show that a ligand can recognize its specific binding site on DNA within a reasonably limited time interval if the number of its reaction centres and the corresponding stability constants are strongly limited