Gerald Weber

Federal University of Minas Gerais | UFMG · Departamento de Física

The mesoscopic Peyrard-Bishop DNA Hamiltonian describes the main molecular interactions with simple potentials, resulting in an efficient calculation of the melting of the duplex helix. It is based on a 2D model which can be simplified to calculate the classical partition function with the transfer-integral technique. At the heart of this approach...

TNA/DNA hybrids share several similarities to RNA/DNA, such as the tendency to form A-type helices and a strong dependency of their thermodynamic properties on purine/pyrimidine ratio. However, unlike RNA/DNA, not much is known about the base-pair properties of TNA. Here, we use a mesoscopic analysis of measured melting temperatures to obtain an es...

Unlike the canonical base pairs AT and GC, the molecular properties of mismatches such as hydrogen bondings and stacking interactions are strongly dependent on the identity of the neighbouring base pairs. As a result, due to the sheer number of possible combinations of mismatches and flanking base pairs, only a fraction of these have been studied i...

Detection of nucleic acids is crucial to the study of their basic properties and consequently to applying this knowledge to the determination of pathologies such as cancer. In this work, our goal is to determine new trends for creating diagnostic tools for cancer driver mutations. Herein, we study a library of natural and modified oligonucleotide d...

Background DNA mismatches can affect the efficiency of PCR techniques if the intended target has mismatches in primers or probes regions. The accepted rule is that mismatches are detrimental as they reduce the hybridization temperatures, yet a more quantitative assessment is rarely performed. Methods We calculate the hybridization temperatures of...

Modified nucleosides are integral to modern drug development, serving as crucial building blocks for creating safer, more potent, and more precisely targeted therapeutic interventions. Nucleobase modifications often confer antiviral and anti-cancer activity as monomers. When incorporated into nucleic acid oligomers, they increase stability against...

Background Viral mutations are the primary cause of mismatches in primer-target hybridisation, affecting the sensibility of molecular techniques, and potentially leading to detection dropouts. Despite its importance, little is known about the quantitative effect of mismatches in primer-target hybridisation. We have used up-to-date and highly detail...

The nearest-neighbor (NN) model is a general tool for the evaluation for oligonucleotide thermodynamic stability. It is primarily used for the prediction of melting temperatures but has also found use in RNA secondary structure prediction and theoretical models of hybridization kinetics. One of the key problems is to obtain the NN parameters from m...

Viral mutations are the primary cause of mismatches in primer-target hybridisation, affecting the sensibility of molecular techniques, potentially leading to detection dropouts. Despite its importance, little is known about the quantitative effect of mismatches in primer-target hybridisation. We use up-to-date and highly detailed thermodynamic mode...

Monovalent and divalent cations play a crucial role in living cells and for molecular techniques such as PCR. Here we evaluate DNA melting temperatures in magnesium (Mg2+) and magnesium‑potassium (Mg2+ + K+) buffers with a mesoscopic model that allows us to estimate hydrogen bonds and stacking interaction potentials. The Mg2+ and Mg2+ + K+ results...

Metal mediated DNA are mismatches where a metal ion bridges the base pairs and are of interest for biosensors. Here, we study T-Hg2+-T, which is known to be stabilized by base pair metal mediated bonds, and C-Ag+-C whose stabilization mechanism is less well understood. We use a mesoscopic model and published melting temperatures of sequences contai...

The coronavirus disease 2019 (COVID-19) pandemic unfolded due to the widespread severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission reinforced the urgent need for affordable molecular diagnostic alternative methods for massive testing screening. We present the clinical validation of a pH-dependent colorimetric reverse transcri...

The COVID-19 pandemics unfolded due to the widespread SARS-CoV-2 transmission reinforced the urgent need for affordable molecular diagnostic alternative methods for massive testing screening. We present the clinical validation of a pH-dependent colorimetric RT-LAMP (reverse transcription loop-mediated isothermal amplification) for SARS-CoV-2 detect...

Mesoscopic models can be used for the description of the thermodynamic properties of RNA duplexes. With the use of experimental melting temperatures, its parametrization can provide important insights into its hydrogen bonds and stacking interactions as has been done for high sodium concentrations. However, the RNA parametrization for lower salt co...

Mismatches are any type of base-pairs other than AT and CG. They are an expected occurrence in PCR primer-target hybridisation and may interfere with the amplification and in some cases even prevent the detection of viruses and other types of target. Given the natural occurrence of mutations it is expected that the number of primer-target mismatche...

Mesoscopic models can be used for the description of the thermodynamic properties of RNA duplexes. With the use of experimental melting temperatures, its parametrization can provide important insights into its hydrogen bonds and stacking interactions as has been done for high sodium concentrations. However, the RNA parametrization for lower salt co...

Mesoscopic models can be used for the description of the thermodynamic properties of RNA duplexes. With the use of experimental melting temperatures, its parametrization can provide important insights into its hydrogen bonds and stacking interactions as has been done for high sodium concentrations. However, the RNA parametrization for lower salt co...

Background DNA mismatches can affect the efficiency of PCR techniques if the intended target has mismatches in primers or probes regions. The accepted rule is that mismatches are detrimental as they reduce the hybridization temperatures, yet a more quantitative assessment is rarely performed. Methods We calculate the hybridization temperatures of...

The Peyrard-Bishop DNA model describes the molecular interactions with simple potentials which allow efficient calculations of melting temperatures. However, it is based on a Hamiltonian that does not consider the helical twist or any other relevant molecular dimensions. Here, we start from a more realistic 3D model and work out several approximati...

TNA/DNA hybrids share several similarities to RNA/DNA, such as the tendency to form A-type helices and a strong dependency of their thermodynamic properties on purine/pyrimidine ratio. However, unlike RNA/DNA, not much is known about the base-pair properties of TNA. Here, we use a mesoscopic analysis of measured melting temperatures to obtain an es...

Unlike the canonical base pairs AT and GC, the molecular properties of mismatches such as hydrogen bondings and stacking interactions are strongly dependent on the identity of the neighbouring base pairs. As a result, due to the sheer number of possible combinations of mismatches and flanking base pairs, only a fraction of these have been studied i...

Structural conversion of cellular prion protein (PrPC) into scrapie PrP (PrPSc) and subsequent aggregation are key events associated with the onset of transmissible spongiform encephalopathies (TSEs). Experimental evidence supports the role of nucleic acids (NAs) in assisting this conversion. Here, we asked whether PrP undergoes liquid‐liquid phase...

Structural conversion of cellular prion protein (PrPC) into scrapie PrP (PrPSc) and subsequent aggregation are key events for the onset of Transmissible Spongiform Encephalopathies (TSEs). Experimental evidences support the role of nucleic acids (NAs) in assisting the protein conversion process. Here, we used the SELEX methodology to identify two 2...

We calculate the nearest-neighbour enthalpies and entropies at 5 salt concentrations of 18 RNA sequences, each for at least 9 different species concentrations, totalling 757 melting temperatures, using a melting temperature optimization method. These new parameters do not need to be salt-corrected and are shown to provide overall improved melting t...

Gene editing technologies sparked a renewed interest in the hybridization of DNA/RNA duplexes, yet little improvement on nearest-neighbour parameters was made over the past two decades. For low sodium concentration no parameter set was yet calculated. Here, we revised the existing experimental datasets and used an expanded set of sequences from whi...

Despite the importance of DNA/RNA hybrids, a mesoscopic approach is still missing. We developed a mesoscopic model for DNA/RNA hybrids and obtained the complete parametrization from published melting temperatures. The new parameters show very clearly the reduced strength of the hydrogen bond of dArU base pairs, resulting in a weakened stabilization...

Simple one-dimensional DNA or RNA mesoscopic models are of interest for their computational efficiency while retaining the key elements of the molecular interactions. However, they only deal with perfectly formed DNA or RNA double helices and consider the intra-strand interactions to be the same on both strands. This makes it difficult to describe...

Cy3 and Cy5 dyes linked to the 5' end of a double stranded DNA molecule are known to attach to both strands in a way that is very similar to an additional base pair and has a stabilizing effect on the oligonucleotide. Here we adapt the Peyrard-Bishop mesoscopic model to incorporate cyanine dyes and use the technique of thermal equivalence to obtain...

BACKGROUND:The RET S836S variant has been associated with early onset and increased risk for metastatic disease in medullary thyroid carcinoma (MTC). However, the mechanism by which this variant modulates MTC pathogenesis is still open to discuss. Of interest, strong linkage disequilibrium (LD) between RET S836S and 3'UTR variants has been reported...

This is the complete user manual for TfReg version 3.0, a free software that implements the Peyrard-Bishop model. New features for this version: optimised parameters for RNA GU, add your own model (requires a bit of programing knowledge), new context-dependent base pair representation and bug fixes.

GU mismatches are crucial to the stability of the RNA double helix and need to be considered in RNA folding algorithms for numerous biotechnological applications. Yet despite its importance many aspects of GU base pairs are still poorly understood. There is also a lack of parametrization which prevents it to be considered in mesoscopic models. Here...

DNA base pairs are known to open more easily at the helix terminal, a process usually called end fraying, the details of which are still poorly understood. Here, we present a mesoscopic model calculation based on available experimental data where we consider separately the terminal base pairs of a DNA duplex. Our results show an important reduction...

Here we apply a technique which uses mesoscopic models to calculate hydrogen bond strengths and stacking interactions from experimental deoxyinosine melting temperatures. Our results confirm a uniform hydrogen bond strength for all deoxyinosine mismatches of the same order of AT base pairs, with the only exception of II mismatches which show a redu...

This is the complete user manual for TfReg version 2.0, a free software that implements the Peyrard-Bishop model. New features for this version: optimised parameters for dexoyinosine, new model MES, new program option nncheck for displaying the base-pair and nearest-neighbour decomposition of sequences.

Complete user manual for VarGibbs which is the free software implementation of the optimization method for obtaining free energy parameters from melting temperatures. This manual describes in detail how to use the software and provides additional information about the optimization method.

Motivation: Free energy nearest-neighbour (NN) thermodynamics is widely used in DNA biochemistry, ranging from the calculation of melting temperatures to the prediction of secondary structures. Methods to calculate NN parameters require the knowledge of total sequence entropies and enthalpies, which are not always available. Results: Here, we im...

Biological databases can be analysed as a complex network which may reveal some its underlying biological mechanisms. Frequently, such databases are identified as scale-free networks or as hierarchical networks depending on connectivity distributions or clustering coefficients. Since these databases do grow over time, one would expect that their ne...

Morse potentials in eV and stacking parameters in eV/Angstrom^2, see TfReg documentation for details of base pair notation.

This is the complete user manual for TfReg version 1.1, a free software that implements the Peyrard-Bishop model.

The Peyrard-Bishop model is a mesoscopic approximation to model DNA and RNA molecules. Several variants of this model exists, from 3D Hamiltonians, including torsional angles, to simpler 2D versions. Currently, we are able to parametrize the 2D variants of the model which allows us to extract important information about the molecule. For example, w...

The mesoscopic statistical physics models, known generically as Peyrard-Bishop (PB) models, have found many applications for the study of oligonucleotide properties. Unfortunately, PB models have not reached a wider non-specialized audience for the lack of freely available software implementations. Here we present an extensible C++ implementation o...

Mirtrons are a special type of pre-miRNA which originate from intronic regions and are spliced directly from the transcript instead of being processed by Drosha. The splicing mechanism is better understood for the processing of mRNA for which was established that there is a characteristic CG content around splice sites. Here we analyse the CG-conte...

Information about molecular interactions in DNA can be obtained from experimental melting temperature data by using mesoscopic statistical physics models. Here, we extend the technique to RNA and show that the new parameters correctly reproduce known properties such as the stronger hydrogen bonds of AU base pairs. We also were able to calculate a c...

Fourier transforms and their associated power spectra are used for detecting periodicities and protein-coding genes and is generally regarded as a well established technique. Many of the periodicities which have been found with this method are quite well understood such as the periodicity of 3 nt which is associated to codon usage. But what is the...

Peyrard-Bishop (PB) models are used for the study of denaturation in DNA. Unfortunately, there is little connection of these models to linear nearest-neighbour models which are extensively used for the calculation of melting temperatures in biochemistry. Here we use the Joyeux-Buyukdagli (JB) model, a variant of the PB model which incorporates stac...

We comment on the flexibility profiles calculated by Zeng et al., and show that these profiles do not represent the local flexibility of the DNA molecule. If one takes into account the physics of elasticity, the averaged flexibility profile show an additional peak which is missed in the original calculation. We show that it is not possible to calcu...

The microscopic flexibility of DNA is a key ingredient for understanding its interaction with proteins and drugs but is still poorly understood and technically challenging to measure. Several experimental methods probe very long DNA samples, but these miss local flexibility details. Others mechanically disturb or modify short molecules and therefor...

Physical statistics models such as the Peyrard-Bishop model are extensively used to study thermodynamic properties of DNA. One of the interesting aspects of this model is that it is a one-dimensional model exhibiting phase transitions which can be continuously changed from smooth to very sharp transitions. The partition function for the Peyrard-Bis...

We present the theory of thermal equivalence in the framework of the Peyrard-Bishop model and some of its anharmonic variants. The thermal equivalence gives rise to a melting index τ which maps closely the experimental DNA melting temperatures for short DNA sequences. We show that the efficient calculation of the melting index can be used to analys...

Transposable elements, or transposons, are DNA segments that are repeated within the same genome and are an important component of the genomes of most species. It is generally believed that they play an important role in evolution and genome restructuring. In this work we built a network based on a score which represents the transposon identity. Th...

Target sequences used. The additional file Sequences.fa.tar contains the sequences used to carry out these experiments. Each file in the archive has the sequence data that we used to create the library for each target sequence. Each file in the archive corresponds to one target, for example, protease.fasta corresponds to the data we used to analyse...

Example probe library generated by this analysis. This additional file Probes.fa.tar contains an example of a probe library set, for the gene np5 at read length 17, generated in this analysis. The files are labeled in a format to indicate the stringency of filtering (GC content followed by Δω). These are also available from the author and on the 4g...

Repeats are a common feature of genomic sequences and much remains to be understood of their origin and structure. The identification of repeated strings in genomic sequences is therefore of importance for a variety of applications in biology. In this paper a new method for finding all repeats and visualizing them in a two-dimensional plot is pres...

Sequencing by hybridisation is an effective method for obtaining large amounts of DNA sequence information at low cost. The efficiency of SBH depends on the design of the probe library to provide the maximum information for minimum cost. Long probes provide a higher probability of non-repeated sequences but lead to an increase in the number of prob...

Within the framework of the Peyrard-Bishop model for DNA melting, sharp denaturation temperature profiles can currently be obtained only if anharmonic base-pair stacking interactions are considered. We show that, when solvent interactions are included, a sharp denaturation of the DNA double helix is obtained without the need for anharmonic nearest-...

The common key to nearly all processes involving DNA is the hybridization and melting of the double helix: from transmission of genetic information and RNA transcription, to polymerase chain reaction and DNA microarray analysis, DNA mechanical nanodevices and DNA computing. Selecting DNA sequences with similar melting temperatures is essential for...

Several methods for ultra high-throughput DNA sequencing are currently under investigation. Many of these methods yield very short blocks of sequence information (reads). Here we report on an analysis showing the level of genome sequencing possible as a function of read length. It is shown that re-sequencing and de novo sequencing of the majority o...

We present a method for obtaining a position-dependent absorption coefficient from near-field scanning optical transmission microscopy. We show that the optical transmission intensity can be combined with the topography, resulting into an absorption coefficient that simplifies the analysis of different materials within a sample. The method is teste...

The electron{acoustic-phonon scattering process in spherical II-VI quantum dots is discussed. The quantized acoustic modes are described in terms of the Lamb's classical theory. We considered two mechanism for the interaction between electrons and acoustic modes: microscopic deformation potential, and macroscopic acoustic deformation, also called t...

We calculate the electron–phonon scattering rates due to coupling with acoustic and longitudinal optical phonons in spherical quantum dots. The quantized optical phonons are described in the dielectric continuum model. The acoustic modes are described in terms of Lamb's classical theory. We have considered two mechanisms for electron–acoustic-phono...

Near field scanning optical microscopy (NSOM) and spectroscopy techniques were used to study the shape and the cell membrane details in bacteria. We present transmission and topographic images for the bacteria Pseudomonas aeruginosa using the Aurora NSOM from ThermoMicroscopes. The P. aeruginosa has been widely studied due to its clinical in many i...

We present near field scanning optical microscopy and spectroscopy images of bacteria. Comparison of simultaneously obtained topographic and transmission images reveal details of the shape and absorption of the laser light by the cell membrane.

We calculate the binding energies for shallow impurities in multiple V-groove GaAs/AlGaAs quantum wires using a variational technique. The carrier ground states are calculated by an effective potential method together with a suitable coordinate transformation which allows the decoupling of the two-dimensional wavefunction. We present results as a f...

Near field scanning optical microscopy (NSOM) was used to study the shape and the cell membrane details in bacteria. We present near field scanning optical transmission and topographic images for the bacteria Pseudomonas aeruginosa. The transmission images show patterns that depends on the thickness and shape of the membrane, thus revealing details...

We calculate the binding energies for shallow impurities in V-groove GaAs/AlxGa1-xAs quantum wires using a variational technique. The carrier ground states are calculated by an effective potential method together with a suitable coordinate transformation that allows the decoupling of the two-dimensional wave function. This method enables a detailed...

We calculate electron-LO-confined and surface phonon scattering rates in CdS1-xSex spherical quantum dots. The phonon modes are described in the frame of the two-mode dielectric continuum model, and the standard k.p formalism is used for treating the electronic band structure. We include the effects of inhomogeneous broadening due to statistical d...

The electron–acoustic-phonon scattering process in spherical II–VI quantum dots is discussed. The quantized acoustic modes are described in terms of Lamb's classical theory for the oscillations of a continuous sphere. The longitudinal spheroidal modes are included owing to their dominant contribution to the acoustic-phonon deformation potential (DP...

We calculate electron-LO-confined and surface phonon scattering rates in CdS [iopmath latex="$_{1-x}{\rm Se}_{x}$"] 1-xSex [/iopmath] spherical quantum dots. The phonon modes are described in the frame of the two-mode dielectric continuum model, and the standard [iopmath latex="${\bi k}. {\bi p}$"] k.p [/iopmath] formalism is used for treating the...

We propose a lateral effective potential which allows a straightforward calculation of electron and hole states in V-groove quantum wires. This effective potential is used together with a suitable coordinate transformation which results in two decoupled one-dimensional Schrödinger equations which are readily solved. The energy levels and wave funct...

We calculate electron-LO-confined and interface-phonon scattering rates in In1-xGaxAs-InP and Hg1-xCdxTe-CdTe quantum wells considering the influence of nonparabolicity on the energy subbands. A simple k.p model is used to take into account this nonparabolicity and a reformulated dielectric continuum slab model is employed to describe the confined...

Time-resolved differential transmission measurements with pump and probe laser pulse durations of less than 100 fs were made on quantum wells with varying well widths. The results were analysed with a phenomenological model using detailed rate equations with five fitting parameters, and comparisons are made with quantum mechanical calculations for...

We present a variational calculation in the effective-mass approximation of the binding energies of shallow donors in a GaAs-GaAlAs quantum wells. The energies and variational wavefunctions associated with the 1s-like ground state as well as some excited states (2s, 2px,y, 2pz, 3s, 3px,y and 3pz-like) are obtained as functions of the position of th...

The authors report time-resolved anti-Stokes Raman scattering measurements of short-period GaAs/AlAs type II superlattices which reveal directly that q approximately 0 confined and interface optical phonons are emitted by electrons when they transfer from the Gamma valley in the GaAs layers to the Xz valley in the AlAs layers in structures where th...

The authors calculate the electron-LO-phonon scattering rates for confined phonon modes associated to intrasubband and intersubband transitions for GaAs-AlxGa1-xAs quantum wells with finite depth. The Huang and Zhu approximation for the confined LO phonon modes, based on a microscopic lattice-dynamic approach, is used and the results are compared w...

The author calculates the scattering rates for intrasubband and intersubband transitions in GaAs-AlAs quantum wells due to interface phonons with an applied longitudinal electric field. The electron-interface-phonon (Frohlich) Hamiltonian used is that obtained from the Fuchs-Kliewer slab model, and the electron envelope wavefunction under the influ...

We calculate the electron capture rates for GaAs-AlxGa1-xAs multiple quantum wells by the emission of confined phonons via electron-phonon (Frohlich) interaction. The carrier capture process as detected by optical measurements is discussed and we show the importance of a knowledge of the details of carrier excitation in order to obtain an appropria...

We calculate the binding energies of 1s, 2s, 2px, 2py, and 2pz donor states bound to X valleys in type-II GaAs-AlAs quantum well structures using an anisotropic variational method that enables us to take into account the effective-mass anisotropy and the quantum confinement. These binding energies present a strong dependence on the effective mass a...

We calculate the binding energies of 2s donor states bound tovalleys in type II GaAs–AlAs quantum well structures using an anisotropic variational method which enables us to take into account the effective mass anisotropy and quantum confinement. For a comparative study, we use two sets of effective masses obtained from different measurements [B. R...

We calculate the Γ→ Xzelectron transfer times due to the emission of confined and interface LO phonons in type-II GaAs–AlAs and AlGaAs–AlAs superlattices. A dielectric continuum model is employed to describe the electron–phonon interaction, and the electron envelope wavefunctions are obtained from a Kronig–Penney model. The calculated transfer time...

We present calculations of Xz electron transfer times in type-II GaAs-AlAs and AlGaAs-AlAs superlattices as a function of the sample temperature. Emission and absorption of confined and interface optical phonons via Fröhlich interaction are considered as the transfer mechanisms. The calculated transfer times and their temperature dependence are in...

The scattering rates for intrasubband and intersubband transitions due to electron–optical-phonon interaction are calculated for GaAs-AlxGa1-xAs quantum wells taking into account the conduction subband nonparabolicity. For the description of the confined- and interface-phonon modes we use a dielectric continuum model and the nonparabolic conduction...

We calculate the Γ → Γ carrier scattering times due to emission of confined and interface optic phonons taking into account the Γ-X hybridization of the electron states for type I GaAs/AlAs quantum well structures. We show that the intersubband transition times increase for well widths where the second GaAs electron subband becomes close in energy...

We calculate the electron-LO-confined-phonon scattering rates in GaAs- AlGaAs quantum wells considering the influence of nonparabolicity on the energy bands. A reformulated slab model is employed to describe the confined phonon and a simple model is assumed to take these nonparabolicity effects into account. An expression for the intra and intersub...

Electron-phonon interaction in polar semiconductor quantum wells attracted a great amount of interest over the last years due to its importance for electronic properties. Particular interest was directed towards LO-phonon confinement which affects significantly the scattering rates in quantum wells. In general, the use of dielectric continuum model...