Subconductance states in a semimicroscopic model for a tetrameric pore

A physical model for a structured tetrameric pore is studied. The pore is modeled as a device composed of four subunits, each one exhibiting two possible states (open and closed). The pore is located within a membrane that separates two reservoirs with ionic solutions. All variables of the model follow physical dynamical equations accounting for the internal structure of the pore, derived from a single energy functional and supplemented with thermal noises. An extensive study of the resulting ionic intensity is performed for different values of the control parameters, mainly membrane potential and reservoir ion concentrations. Two possible physical devices are studied: voltage-gated (including a voltage sensor in each subunit) and non-voltage-gated pores. The ionic flux through the pore exhibits several distinct dynamical configurations, in particular subconductance states, which indicate very different dynamical internal states of the subunits. Such subconductance states become much easier to observe in sensorless pores. These results are compared with available experimental data on tetrameric K channels and analytical predictions.

Lenalidomide in combination with R-ESHAP in patients with relapsed or refractory diffuse large B-cell lymphoma: A phase 2 study from GELTAMO

Diffuse large B-cell lymphoma (DLBCL) patients with relapsed or refractory (RR) disease have poor outcomes with current salvage regimens. We conducted a phase 2 trial to analyse the safety and efficacy of adding lenalidomide to R-ESHAP (LR-ESHAP) in patients with RR DLBCL. Subjects received 3 cycles of lenalidomide 10 mg/day on days 1-14 of every 21-day cycle, in combination with R-ESHAP at standard doses. Responding patients underwent autologous stem-cell transplantation (ASCT). The primary endpoint was the overall response rate (ORR) after 3 cycles. Centralized cell-of-origin (COO) classification was performed. Forty-six patients were included. The ORR after LR-ESHAP was 67% (35% of patients achieved complete remission). Patients with primary refractory disease (n = 26) had significantly worse ORR than patients with non-refractory disease (54% vs. 85%, p = 0.031). No differences in response rates according to the COO were observed. Twenty-eight patients (61%) underwent ASCT. At a median follow-up of 41 months, the estimated 3-year PFS and OS were 42% and 48%, respectively. The most common grade ≥3 adverse events were thrombocytopenia (70% of patients), neutropenia (67%) and anaemia (35%). There were no treatment-related deaths during LR-ESHAP cycles. In conclusion, LR-ESHAP is a feasible salvage regimen with promising efficacy results for patients with RR DLBCL.

Landau theory for cellular patterns driven by lateral inhibition interaction

The phenomenology of Landau theory with spatial coupling through diffusion has been widely used in the study of phase transitions and patterning. Here we follow this theory and apply it to study theoretically and numerically continuous and discontinuous transitions to periodic spatial cellular patterns driven by lateral inhibition coupling. As opposed to diffusion, lateral inhibition coupling drives differences between adjacent cells. We analyze the appearance of errors in these patterns (disordered metastable states) and propose mechanisms to prevent them. These mechanisms are based on a temporal-dependent lateral inhibition coupling strength, which can be mediated, among others, by gradients of diffusing molecules. The simplicity and generality of the framework used herein is expected to facilitate future analyses of additional phenomena taking place through lateral inhibition interactions in more complex scenarios.

Diagnostic delay and outcome in immunocompetent patients with primary central nervous system lymphoma in Spain: a multicentric study

INTRODUCTION

To assess the management of immunocompetent patients with primary central nervous system lymphomas (PCNSL) in Spain.

METHODS

Retrospective analysis of 327 immunocompetent patients with histologically confirmed PCNSL diagnosed between 2005 and 2014 in 27 Spanish hospitals.

RESULTS

Median age was 64 years (range: 19-84; 33% ≥ 70 years), 54% were men, and 59% had a performance status (PS) ≥ 2 at diagnosis. Median delay to diagnosis was 47 days (IQR 24-81). Diagnostic delay > 47 days was associated with PS ≥ 2 (OR 1.99; 95% CI 1.13-3.50; p = 0.016) and treatment with corticosteroids (OR 2.47; 95% CI 1.14-5.40; p = 0.023), and it did not improve over the years. Patients treated with corticosteroids (62%) had a higher risk of additional biopsies (11.7% vs 4.0%, p = 0.04) but corticosteroids withdrawal before surgery did not reduce this risk and increased the diagnostic delay (64 vs 40 days, p = 0.04). Median overall survival (OS) was 8.9 months [95% CI 5.9-11.7] for the whole series, including 52 (16%) patients that were not treated, and 14.1 months (95%CI 7.7-20.5) for the 240 (73.4%) patients that received high-dose methotrexate (HD-MTX)-based chemotherapy. Median OS was shorter in patients ≥ 70 years (4.1 vs. 13.4 months; p < 0.0001). Multivariate analysis identified age ≥ 65 years, PS ≥ 2, no treatment, and cognitive/psychiatric symptoms at diagnosis as independent predictors of short survival.

CONCLUSIONS

Corticosteroids withdrawal before surgery does not decrease the risk of a negative biopsy but delays diagnosis. In this community-based study, only 73.4% of patients could receive HD-MTX-based chemotherapy and OS remains poor, particularly in elderly patients ≥ 70 years.

A Brownian Ratchet Model Explains the Biased Sidestepping of Single-Headed Kinesin-3 KIF1A

The kinesin-3 motor KIF1A is involved in long-ranged axonal transport in neurons. To ensure vesicular delivery, motors need to navigate the microtubule lattice and overcome possible roadblocks along the way. The single-headed form of KIF1A is a highly diffusive motor that has been shown to be a prototype of a Brownian motor by virtue of a weakly bound diffusive state to the microtubule. Recently, groups of single-headed KIF1A motors were found to be able to sidestep along the microtubule lattice, creating left-handed helical membrane tubes when pulling on giant unilamellar vesicles in vitro. A possible hypothesis is that the diffusive state enables the motor to explore the microtubule lattice and switch protofilaments, leading to a left-handed helical motion. Here, we study the longitudinal rotation of microtubules driven by single-headed KIF1A motors using fluorescence-interference contrast microscopy. We find an average rotational pitch of ≃1.5μm, which is remarkably robust to changes in the gliding velocity, ATP concentration, microtubule length, and motor density. Our experimental results are compared to stochastic simulations of Brownian motors moving on a two-dimensional continuum ratchet potential, which quantitatively agree with the fluorescence-interference contrast experiments. We find that single-headed KIF1A sidestepping can be explained as a consequence of the intrinsic handedness and polarity of the microtubule lattice in combination with the diffusive mechanochemical cycle of the motor.

Integrating genomic alterations in diffuse large B-cell lymphoma identifies new relevant pathways and potential therapeutic targets

Genome studies of diffuse large B-cell lymphoma (DLBCL) have revealed a large number of somatic mutations and structural alterations. However, the clinical significance of these alterations is still not well defined. In this study, we have integrated the analysis of targeted next-generation sequencing of 106 genes and genomic copy number alterations (CNA) in 150 DLBCL. The clinically significant findings were validated in an independent cohort of 111 patients. Germinal center B-cell and activated B-cell DLBCL had a differential profile of mutations, altered pathogenic pathways and CNA. Mutations in genes of the NOTCH pathway and tumor suppressor genes (TP53/CDKN2A), but not individual genes, conferred an unfavorable prognosis, confirmed in the independent validation cohort. A gene expression profiling analysis showed that tumors with NOTCH pathway mutations had a significant modulation of downstream target genes, emphasizing the relevance of this pathway in DLBCL. An in silico drug discovery analysis recognized 69 (46%) cases carrying at least one genomic alteration considered a potential target of drug response according to early clinical trials or preclinical assays in DLBCL or other lymphomas. In conclusion, this study identifies relevant pathways and mutated genes in DLBCL and recognizes potential targets for new intervention strategies.

Autologous stem cell transplantation (ASCT) in patients with mantle cell lymphoma: a retrospective study of the Spanish lymphoma group (GELTAMO)

Guidelines recommend autologous stem cell transplantation (ASCT) consolidation in first complete or partial response after regimens including rituximab (R) and high-dose AraC (HDAC), but its use beyond that response is questioned. We present a retrospective analysis of 268 patients with MCL who received ASCT. With a median follow-up for survival patients of 54 months, progression-free survival and overall survival for the whole series were 38 and 74 months, respectively, and for patients transplanted in first CR 49 and 97 months, respectively. Patients without CR before transplant were analyzed separately, those who achieved CR after transplantation had better PFS (48 vs 0.03 months, p < 0.001) and OS (92 vs 16 months, p < 0.001) than the remaining. In univariate analysis, first CR at transplant (p = 0.01) and prior rituximab (p = 0.02) were the variables associated with PFS. For OS, the same variables resulted significant (p = 0.03 and p < 0.001, respectively). In multivariate analysis, only the status at transplant (first CR) remained significant. This retrospective study concludes that ASCT consolidation in first CR induces high survival rates. In other stages of disease, the need of ASCT as consolidation may be questioned.

A Tunable Magnetic Domain Wall Conduit Regulating Nanoparticle Diffusion

We demonstrate a general and robust method to confine on a plane strongly diffusing nanoparticles in water by using size tunable magnetic channels. These virtual conduits are realized with pairs of movable Bloch walls located within an epitaxially grown ferrite garnet film. We show that once inside the magnetic conduit the particles experience an effective local parabolic potential in the transverse direction, while freely diffusing along the conduit. The stiffness of the magnetic potential is determined as a function of field amplitude that varies the width of the magnetic channel. Precise control of the degree of confinement is demonstrated by tuning the applied field. The magnetic conduit is then used to realize single files of nonpassing particles and to induce periodic condensation of an ensemble of particles into parallel stripes in a completely controllable and reversible manner.

Pattern selection by dynamical biochemical signals

The development of multicellular organisms involves cells to decide their fate upon the action of biochemical signals. This decision is often spatiotemporally coordinated such that a spatial pattern arises. The dynamics that drive pattern formation usually involve genetic nonlinear interactions and positive feedback loops. These complex dynamics may enable multiple stable patterns for the same conditions. Under these circumstances, pattern formation in a developing tissue involves a selection process: why is a certain pattern formed and not another stable one? Herein we computationally address this issue in the context of the Notch signaling pathway. We characterize a dynamical mechanism for developmental selection of a specific pattern through spatiotemporal changes of the control parameters of the dynamics, in contrast to commonly studied situations in which initial conditions and noise determine which pattern is selected among multiple stable ones. This mechanism can be understood as a path along the parameter space driven by a sequence of biochemical signals. We characterize the selection process for three different scenarios of this dynamical mechanism that can take place during development: the signal either 1) acts in all the cells at the same time, 2) acts only within a cluster of cells, or 3) propagates along the tissue. We found that key elements for pattern selection are the destabilization of the initial pattern, the subsequent exploration of other patterns determined by the spatiotemporal symmetry of the parameter changes, and the speeds of the path compared to the timescales of the pattern formation process itself. Each scenario enables the selection of different types of patterns and creates these elements in distinct ways, resulting in different features. Our approach extends the concept of selection involved in cellular decision-making, usually applied to cell-autonomous decisions, to systems that collectively make decisions through cell-to-cell interactions.

Central nervous system prophylaxis with intrathecal liposomal cytarabine in a subset of high-risk patients with diffuse large B-cell lymphoma receiving first line systemic therapy in a prospective trial

The dissemination in the central nervous system (CNS) is an uncommon but fatal complication occurring in patients with diffuse large B-cell lymphoma (DLBCL). Standard prophylaxis has been demonstrated to reduce CNS relapse and improve survival rates. Intrathecal (IT) liposomal cytarabine allows maintaining elevated drug levels in the cerebrospinal fluid for an extended period of time. Data on the efficacy and safety of liposomal cytarabine as CNS prophylaxis in patients with DLBCL are still insufficient. The objective of the present study was to evaluate the effectiveness and safety of the prophylaxis with IT liposomal cytarabine in prevention of CNS relapse in high-risk patients with DLBCL who were included in a trial of first line systemic therapy with 6 cycles of dose-dense R-CHOP every 14 days. Twenty-four (18.6 %) out of 129 patients were identified to have risk factors for CNS involvement, defined as follows: >30 % bone marrow infiltration, testes infiltration, retroperitoneal mass ≥10 cm, Waldeyer ring, or bulky cervical nodes involvement. Liposomal cytarabine (50 mg) was administered by lumbar puncture the first day of the 1st, 2nd, and 6th cycle of R-CHOP14 scheme. Among 70 IT infusions, grade 3-4 adverse events reported were headache (one patient) and nausea/vomiting (one patient). With a median follow-up of 40.1 months, no CNS involvement by DLBCL was observed in any patient. In conclusion, IT liposomal cytarabine is safe, feasible, and effective for CNS prophylaxis, causing few associated risks and little discomfort to patients with DLBCL.

Brownian colloids in underdamped and overdamped regimes with nonhomogeneous temperature

The motion of Brownian particles when temperature is spatially dependent is studied by stochastic simulations and theoretical analysis. Nonequilibrium steady probability distributions P(st)(z,v) for both underdamped and overdamped regimes are analyzed. The existence of local kinetic energy equipartition theorem is also discussed. The transition between both regimes is characterized by a dimensionless friction parameter. This study is applied to three physical systems of colloidal particles.

Lymphomatoid granulomatosis of central nervous system and lung driven by epstein barr virus proliferation: successful treatment with rituximab-containing chemotherapy

Lymphomatoid granulomatosis (LYG) is a very rare Epstein-Barr virus (EBV) associated B-cell lymphoproliferative disorder. We report the case of a 41-year-old man who presented with fever and respiratory symptoms. Computed tomography showed multiple nodules in both lung fields. Polymerase chain reaction (PCR) analysis for EBV was positive in bronchoalveolar lavage and biopsy of lung node yielded a diagnosis of LYG, grade III. Shortly after initiation of treatment with agressive chemotherapy, neurological deterioration appeared. Neuroimaging findings revealed hydrocephalus and PCR analysis of the cerebrospinal fluid (CSF) was positive for EBV. Treatment with intravenous rituximab led to rapid reduction of EBV load in CSF, along with clinical and radiological improvement. After completion of treatment with immunochemotherapy, an autologous stem cell transplantation was performed. Patient stays in remission 18 months after diagnosis.

Transport and diffusion of overdamped Brownian particles in random potentials

We present a numerical study of the anomalies in transport and diffusion of overdamped Brownian particles in totally disordered potential landscapes in one and in two dimensions. We characterize and analyze the effects of three different disordered potentials. The anomalous regimes are characterized by the time exponents that exhibit the statistical moments of the ensemble of particle trajectories. The anomaly in the transport is always of the subtransport type, but diffusion presents a greater variety of anomalies: Both subdiffusion and superdiffusion are possible. In two dimensions we present a mixed anomaly: subdiffusion in the direction perpendicular to the force and superdiffusion in the parallel direction.

Theoretical study of a molecular turbine

We present an analytic and stochastic simulation study of a molecular engine working with a flux of particles as a turbine. We focus on the physical observables of velocity, flux, power, and efficiency. The control parameters are the external conservative force and the particle densities. We revise a simpler previous study by using a more realistic model containing multiple equidistant vanes complemented by stochastic simulations of the particles and the turbine. Here we show that the effect of the thermal fluctuations into the flux and the efficiency of these nanometric devices are relevant to the working scale of the system. The stochastic simulations of the Brownian motion of the particles and turbine support the simplified analytical calculations performed.

Unconventional dynamic hysteresis in a periodic assembly of paramagnetic colloids

Dynamic hysteresis phenomena are widespread in physical sciences and describe the complex behavior of systems driven out of equilibrium by a periodic forcing. We use here paramagnetic colloids above a stripe-patterned garnet film as the model system to study dynamic hysteresis, the latter induced when the particles are periodically translated by an oscillating magnetic field. In contrast to the expected behavior for a bistable system, we observe that the area of the hysteresis loop decreases by increasing the driving frequency and reduces to zero for frequencies higher than 5-7s(-1). To explain the experimental results, we develop a simple model based on an overdamped Brownian particle driven by a periodic potential with an oscillating amplitude.

[Locating pulmonary nodules with a computed axial tomography-guided harpoon prior to videothoracoscopic resection. Experience with 52 cases]

OBJECTIVE

Videothoracoscopic (VTC) resection of peripheral pulmonary nodules (PN) occasionally requires performing a mini-thoracotomy to locate them using palpation. The aim of this study is to evaluate the usefulness of inserting a CT-guided harpoon as a method for locating PN prior to surgery.

MATERIAL AND METHODS

A study was conducted on a total of 52 patients who were scheduled for locating 55 PN prior to surgery by inserting a CT-guided harpoon, from November 2004 to January 2011.

RESULTS

Of the 52 patients, of whom 35 had a history of cancer, 31 were male and 21 were female, with ages between 28 and 84 years (mean: 62.2 years) with a PN <20mm (mean: 9.57mm). A total of 55 harpoons were inserted (3 patients had 2 simultaneous harpoons). Using the VTC it was observed that 52 harpoons were correctly anchored to the PN. There were no complications. In the group of 35 patients with an oncology history, the nodules were malignant in 26 cases (74.3%), and there were 17 (70.6%) with malignant PN in those with no oncology history. The hospital stay varied between 4 and 72h, with 19 patients (36.5%) included in a one-day surgery program.

CONCLUSIONS

The preoperative identification of peripheral pulmonary nodules enables them to be removed directly with VTC. The insertion of a CT-guided harpoon in the PN is a safe and effective procedure that can be performed in a one-day surgery program.

Asymmetric stochastic switching driven by intrinsic molecular noise

Low-copy-number molecules are involved in many functions in cells. The intrinsic fluctuations of these numbers can enable stochastic switching between multiple steady states, inducing phenotypic variability. Herein we present a theoretical and computational study based on Master Equations and Fokker-Planck and Langevin descriptions of stochastic switching for a genetic circuit of autoactivation. We show that in this circuit the intrinsic fluctuations arising from low-copy numbers, which are inherently state-dependent, drive asymmetric switching. These theoretical results are consistent with experimental data that have been reported for the bistable system of the gallactose signaling network in yeast. Our study unravels that intrinsic fluctuations, while not required to describe bistability, are fundamental to understand stochastic switching and the dynamical relative stability of multiple states.

Molecular motors in conservative and dissipative regimes

We present a theoretical study of a rotatory molecular motor under a conservative torque regime. We show that conservative and dissipative regimes present a different observable phenomenology. Our approach starts with a preliminary deterministic calculation of the motor cycle, which is complemented with stochastic simulations of a Langevin equation under a flashing ratchet potential. Finally, by using parameter values obtained from independent experimental information, our theoretical predictions are compared with experimental data of the F(1)-ATPase motor of the Bacillus PS3.

Brownian colloidal particles: Ito, Stratonovich, or a different stochastic interpretation

Recent experiments on Brownian colloidal particles have been studied theoretically in terms of overdamped Langevin equations with multiplicative white noise using an unconventional stochastic interpretation. Complementary numerical simulations of the same system are well described using the conventional Stratonovich interpretation. Here we address this dichotomy from a more generic starting point: the underdamped Langevin equation and its corresponding Fokker-Planck equation.

Weak disorder: anomalous transport and diffusion are normal yet again

We carry out a detailed study of the motion of particles driven by a constant external force over a landscape consisting of a periodic potential corrugated by a small amount of spatial disorder. We observe anomalous behavior in the form of subdiffusion and superdiffusion and even subtransport over very long time scales. Recent studies of transport over slightly random landscapes have focused only on parameters leading to normal behavior, and while enhanced diffusion has been identified when the external force approaches the critical value associated with the transition from locked to running solutions, the regime of anomalous behavior had not been recognized. We provide a qualitative explanation for the origin of these anomalies, and make connections with a continuous time random walk approach.

Phase-response approach to firing-rate selectivity in neurons with subthreshold oscillations

Subthreshold oscillations provide neurons with a filtering mechanism that allows their membrane potential to respond selectively to oscillatory currents depending on their frequency. On the other hand, the phase of such oscillations is known to affect the precise timing at which action potentials can be elicited by input spikes. Here we study the combined effect of these two properties by examining the response of a model neuron to periodic spike trains of defined frequency, in the presence of subthreshold oscillatory activity. Numerical results show a marked resonance with the input firing rate, irrespective of the initial relative phase between the input spike train and the intrinsic subthreshold oscillation. This behavior can be understood in terms of a delayed phase transition curve, from which an iterative map can be built that describes the evolution of the phase response to the periodic succession of input spike perturbations. Depending on the input period, the map exhibits stationary, periodic, or chaotic dynamics that predict in a quantitative way the response of the neuron to the spike train. Propagation of the spike train through a chain of neurons is also examined, and the resonant behavior is seen to be enhanced upon propagation.

Theoretical analysis of the F(1)-ATPase experimental data

F(1)-ATPase is a rotatory molecular motor fueled by ATP nucleotides. Different loads can be attached to the motor axis to show that it rotates in main discrete steps of 120 degrees with substeps of approximately 80 degrees and 40 degrees . Experimental data show the dependence on the mean rotational velocity omega with respect to the external control parameters: the nucleotide concentration [ATP] and the friction of the load gamma(L). In this work we present a theoretical analysis of the experimental data whose main results are: 1), A derivation of a simple analytical formula for omega([ATP], gamma(L)) that compares favorably with experiments; 2), The introduction of a two-state flashing ratchet model that exhibits experimental phenomenology of a greater specificity than has been, to our knowledge, previously available; 3), The derivation of an argument to obtain the values of the substep sizes; 4), An analysis of the energy constraints of the model; and 5), The theoretical analysis of the coupling ratio between the ATP consumed and the success of a forward step. We also discuss the compatibility of our approach with recent experimental observations.

Stochastic algorithms for discontinuous multiplicative white noise

Stochastic differential equations with multiplicative noise need a mathematical prescription due to different interpretations of the stochastic integral. This fact implies specific algorithms to perform numerical integrations or simulations of the stochastic trajectories. Moreover, if the multiplicative noise function is not continuous then the standard algorithms cannot be used. We present an explicit algorithm to avoid this problem and we apply it to a well controlled example. Finally, we discuss on the existence of higher-order algorithms for this specific situation.

Analysis of the nucleotide-dependent conformations of kinesin-1 in the hydrolysis cycle

Kinesin-1 motion on a microtubule (MT) is still receiving a great attention due to its relevance in understanding molecular motion triggered by adenosine triphosphate (ATP) hydrolysis. Recent experimental data on kinesin-tubulin-nucleotide interactions have clarified some of the conformational details involved in the hydrolysis process [T. Mori et al., Nature (London) 450, 750 (2007)]. Specifically, fluorescence resonance energy transfer was used to measure the affinity of motor domains to tubulin heterodimers. Our work is directly devoted to understand and reproduce the main output of these experiments as well as to go beyond and give a global dynamical picture of the whole hydrolysis cycle. We predict that phosphate groups have the ability to confine to the tubulin domains in order to explain the delay between ATP hydrolysis and head detaching, which seems crucial for the achievement of processivity. In our approach me make use of chemical kinetics complemented with stochastic molecular simulations of the elements involved.

Diffusion coefficient in periodic and random potentials

Transport and diffusion of particles on modulated surfaces is a nonequilibrium problem which is receiving a great deal of attention due to its technological applications, but analytical calculations are scarce. In earlier work, we developed a perturbative approach to begin to provide an analytic platform for predictions about particle trajectories over such surfaces. In some temperature and forcing regimes, we successfully reproduced results for average particle velocities obtained from numerical simulations. In this paper, we extend the perturbation theory to the calculation of higher moments, in particular the diffusion tensor and the skewness. Numerical simulations are used to check the domain of validity of the perturbative approach.

Theoretical study of a membrane channel gated by ATP

We study channel transport across biomembranes. We propose a model that couples the diffusive dynamics with the gating process via a two-state ratchet mechanism. This gating process is governed by ATP binding and hydrolysis, and the process exhibits Michaelis-Menten enzymatic kinetics. The particle flow and permeability of the channel are studied both analytically and numerically in the steady-state regime, while working between fixed concentrations. The results are compared with simpler models and with experimental data. Also, a simulation framework, that allows high flexibility in parameter exploration, is introduced.

Brownian pump powered by a white-noise flashing ratchet

A Brownian pump of particles powered by a stochastic flashing ratchet mechanism is studied. The pumping device is embedded in a finite region and bounded by particle reservoirs. In the steady state, we exactly calculate the spatial density profile, the concentration ratio between both reservoirs and the particle flux. We propose a simulation framework for the consistent evaluation of such observable quantities.

Self-sustained spatiotemporal oscillations induced by membrane-bulk coupling

We propose a novel mechanism leading to spatiotemporal oscillations in extended systems that does not rely on local bulk instabilities. Instead, oscillations arise from the interaction of two subsystems of different spatial dimensionality. Specifically, we show that coupling a passive diffusive bulk of dimension d with an excitable membrane of dimension d-1 produces a self-sustained oscillatory behavior. An analytical explanation of the phenomenon is provided for d=1. Moreover, in-phase and antiphase synchronization of oscillations are found numerically in one and two dimensions. This novel dynamic instability could be used by biological systems such as cells, where the dynamics on the cellular membrane is necessarily different from that of the cytoplasmic bulk.

Dispersionless transport in a washboard potential

We study and characterize a new dynamical regime of underdamped particles in a tilted washboard potential. We find that for small friction in a finite range of forces the particles move essentially nondispersively, that is, coherently, over long intervals of time. The associated distribution of the particle positions moves at an essentially constant velocity and is far from Gaussian-like. This new regime is complementary to, and entirely different from, well-known nonlinear response and large dispersion regimes observed for other values of the external force.

Tight coupling in thermal Brownian motors

We study analytically a thermal Brownian motor model and calculate exactly the Onsager coefficients. We show how the reciprocity relation holds and that the determinant of the Onsager matrix vanishes. Such a condition implies that the device is built with tight coupling. This explains why Carnot's efficiency can be achieved in the limit of infinitely slow velocities. We also prove that the efficiency at maximum power has the maximum possible value, which corresponds to the Curzon-Alhborn bound. Finally, we discuss the model acting as a Brownian refrigerator.

Analytical approach to sorting in periodic and random potentials

There has been a recent revolution in the ability to manipulate micrometer-sized objects on surfaces patterned by traps or obstacles of controllable configurations and shapes. One application of this technology is to separate particles driven across such a surface by an external force according to some particle characteristic such as size or index of refraction. The surface features cause the trajectories of particles driven across the surface to deviate from the direction of the force by an amount that depends on the particular characteristic, thus leading to sorting. While models of this behavior have provided a good understanding of these observations, the solutions have so far been primarily numerical. In this paper we provide analytic predictions for the dependence of the angle between the direction of motion and the external force on a number of model parameters for periodic as well as random surfaces. We test these predictions against exact numerical simulations.

Heat fluctuations in Brownian transducers

The heat fluctuation probability distribution function in Brownian transducers operating between two heat reservoirs is studied. We find, both analytically and numerically, that the recently proposed fluctuation theorem for heat exchange [C. Jarzynski and D. K. Wojcik, Phys. Rev. Lett. 92, 230602 (2004)] has to be applied carefully when the coupling mechanism between both baths is considered. We also conjecture how to extend such a relation when an external work is present.

Exported oscillator competition: a concept to analyze complex rhythms

We study the interaction between two independent nonlinear oscillators competing through a neutral excitable element. The first oscillator, completely deterministic, acts as a normal pacemaker sending pulses to the neutral element which fires when it is excited by these pulses. The second oscillator, endowed with some randomness, though unable to make the excitable element to beat, leads to the occasional suppression of its firing. The missing beats or errors are registered and their statistics analyzed in terms of the noise intensity and the periods of both oscillators. This study is inspired in some complex rhythms such as a particular class of heart arrhythmia.

Physical analysis of a processive molecular motor: the conventional kinesin

We present a model that allows for the derivation of the experimentally accessible observables: spatial steps, mean velocity, stall force, useful power, efficiency and randomness, etc. as a function of the [adenosine triphosphate] concentration and an external load F. The model presents a minimum of adjustable parameters and the theoretical predictions compare well with the available experimental results.

Sorting on periodic surfaces

Particles moving on crystalline surfaces and driven by external forces or flow fields can acquire velocities along directions that deviate from that of the external force. This effect depends upon the characteristics of the particles, most notably particle size or particle index of refraction, and can therefore be (and has been) used to sort different particles. We introduce a simple model for particles subject to thermal fluctuations and moving in appropriate potential landscapes. Numerical results are compared to recent experiments on landscapes produced with holographic optical tweezers and microfabricated technology. Our approach clarifies the relevance of different parameters, the direction and magnitude of the external force, particle size, and temperature.

Symmetric Brownian motor

In this paper, we present a model of a symmetric Brownian motor which changes the sign of its velocity when the temperature gradient is inverted. The velocity, external work, and efficiency are studied as a function of the temperatures of the baths and other relevant parameters. The motor shows a current reversal when another parameter (a phase shift) is varied. Analytical predictions and results from numerical simulations are performed and agree very well. Generic properties of this type of motor are discussed.

Suppression of scroll wave turbulence by noise

Rotating scroll waves are dynamical spatiotemporal structures characteristic of three-dimensional active media. It is well known that, under low excitability conditions, scroll waves develop an intrinsically unstable dynamical regime that leads to a highly disorganized pattern of wave propagation. Such a "turbulent" state bears some resemblance to fibrillation states in cardiac tissue. We show here that this unstable regime can be controlled by using a spatially distributed random forcing superimposed on a control parameter of the system. Our results are obtained from numerical simulations but an explicit analytical argument that rationalizes our observations is also presented.

From subdiffusion to superdiffusion of particles on solid surfaces

We present a numerical and partially analytical study of classical particles obeying a Langevin equation that describes diffusion on a surface modeled by a two-dimensional potential. The potential may be either periodic or random. Depending on the potential and the damping, we observe superdiffusion, large-step diffusion, diffusion, and subdiffusion. Superdiffusive behavior is associated with low damping and is in most cases transient, albeit often long. Subdiffusive behavior is associated with highly damped particles in random potentials. In some cases subdiffusive behavior persists over our entire simulation and may be characterized as metastable. In any case, we stress that this rich variety of behaviors emerges naturally from an ordinary Langevin equation for a system described by ordinary canonical Maxwell-Boltzmann statistics.

Diffusion on a solid surface: anomalous is normal

We present a numerical study of classical particles diffusing on a solid surface. The particles' motion is modeled by an underdamped Langevin equation with ordinary thermal noise. The particle-surface interaction is described by a periodic or a random two-dimensional potential. The model leads to a rich variety of different transport regimes, some of which correspond to anomalous diffusion such as has recently been observed in experiments and Monte Carlo simulations. We show that this anomalous behavior is controlled by the friction coefficient and stress that it emerges naturally in a system described by ordinary canonical Maxwell-Boltzmann statistics.

Modelization of surface diffusion of a molecular dimer

A simple model for a dimer molecular diffusion on a crystalline surface, as a function of temperature, is presented. The dimer is formed by two particles coupled by a quadratic potential. The dimer diffusion is modeled by an overdamped Langevin equation in the presence of a two-dimensional periodic potential. Numerical simulation's results exhibit some dynamical properties observed, for example, in Si2 diffusion on a silicon [100] surface. They can be used to predict the value of the effective friction parameter. Comparison between our model and experimental measurements is presented.

Plankton blooms induced by turbulent flows

Plankton play an important role in the ecology of the ocean and the climate because of their participation in the global carbon cycle at the base of the food chain. However, damaging plankton blooms can sometimes occur and are initially characterized by sudden transient increases in the phytoplankton population. They are thought to be driven by several effects, such as seasonal variations in temperature and salinity, and nutrient mixing. Furthermore, phytoplankton and zooplankton have different buoyancy properties, leading to a differential response in turbulent environments. In this paper, we investigate this effect in a model of advected plankton dynamics. We find that, over a range of parameter values, flows of marine species subjected to inertial/viscous forces naturally lead to patchiness and, in turn, periodically sustained plankton blooms.

Intrinsic noise-induced phase transitions: beyond the noise interpretation

We discuss intrinsic noise effects in stochastic multiplicative-noise partial differential equations, which are qualitatively independent of the noise interpretation (Itô vs Stratonovich), in particular in the context of noise-induced ordering phase transitions. We study a model which, contrary to all cases known so far, exhibits such ordering transitions when the noise is interpreted not only according to Stratonovich, but also to Itô. The main feature of this model is the absence of a linear instability at the transition point. The dynamical properties of the resulting noise-induced growth processes are studied and compared in the two interpretations and with a reference Ginzburg-Landau-type model. A detailed discussion of a different numerical algorithm valid for both interpretations is also presented.

Confinement of discrete breathers in inhomogeneously profiled nonlinear chains

We investigate numerically the scattering of a moving discrete breather on a pair of junctions in a Fermi-Pasta-Ulam chain. These junctions delimit an extended region with different masses of the particles. We consider (i) a rectangular trap, (ii) a wedge shaped trap, and (iii) a smoothly varying convex or concave mass profile. All three cases lead to DB confinement, with the ease of trapping depending on the profile of the trap. We also study the collision and trapping of two DBs within the profile as a function of trap width, shape, and approach time at the two junctions. The latter controls whether one or both DBs are trapped.

Noise-driven mechanism for pattern formation

We extend the mechanism for noise-induced phase transitions proposed by Ibañes et al. [Phys. Rev. Lett. 87, 020601 (2001)] to pattern formation phenomena. In contrast with known mechanisms for pure noise-induced pattern formation, this mechanism is not driven by a short-time instability amplified by collective effects. The phenomenon is analyzed by means of a modulated mean field approximation and numerical simulations.

Coherence and anticoherence resonance tuned by noise

We present numerical evidence and a theoretical analysis of the appearance of anticoherence resonance induced by noise, not predicted in former analysis of coherence resonance. We have found that this phenomenon occurs for very small values of the intensity of the noise acting on an excitable system, and we claim that this is a universal signature of a nonmonotonous relaxational behavior near its oscillatory regime. Moreover, we demonstrate that this new phenomenon is totally compatible with the standard situation of coherence resonance appearing at intermediate values of noise intensity.

Interaction of a discrete breather with a lattice junction

We study the scattering of a moving discrete breather (DB) on a junction in a Fermi-Pasta-Ulam chain consisting of two segments with different masses of the particles. We consider four distinct cases: (i) a light-heavy (abrupt) junction in which the DB impinges on the junction from the segment with lighter mass, (ii) a heavy-light junction, (iii) an up mass ramp in which the mass in the heavier segment increases continuously as one moves away from the junction point, and (iv) a down mass ramp. Depending on the mass difference and DB characteristics (frequency and velocity), the DB can either reflect from, or transmit through, or get trapped at the junction or on the ramp. For the heavy-light junction, the DB can even split at the junction into a reflected and a transmitted DB. The latter is found to subsequently split into two or more DBs. For the down mass ramp the DB gets accelerated in several stages, with accompanying radiation (phonons). These results are rationalized by calculating the Peierls-Nabarro barrier for the various cases. We also point out implications of our results in realistic situations such as electron-phonon coupled chains.

Pulse propagation sustained by noise in arrays of bistable electronic circuits

One-dimensional arrays of nonlinear electronic circuits are shown to support propagation of pulses when operating in a locally bistable regime, provided the circuits are under the influence of a global noise. These external random fluctuations are applied to the parameter that controls the transition between bistable and monostable dynamics in the individual circuits. As a result, propagating fronts become destabilized in the presence of noise, and the system self-organizes to allow the transmission of pulses. The phenomenon is also observed in weakly coupled arrays, when propagation failure arises in the absence of noise.