Predicting a Protein's Stability under a Million Mutations

Stabilizing proteins is a foundational step in protein engineering. However, the evolutionary pressure of all extant proteins makes identifying the scarce number of mutations that will improve thermodynamic stability challenging. Deep learning has recently emerged as a powerful tool for identifying promising mutations. Existing approaches, however, are computationally expensive, as the number of model inferences scales with the number of mutations queried. Our main contribution is a simple, parallel decoding algorithm. Our Mutate Everything is capable of predicting the effect of all single and double mutations in one forward pass. It is even versatile enough to predict higher-order mutations with minimal computational overhead. We build Mutate Everything on top of ESM2 and AlphaFold, neither of which were trained to predict thermodynamic stability. We trained on the Mega-Scale cDNA proteolysis dataset and achieved state-of-the-art performance on single and higher-order mutations on S669, ProTherm, and ProteinGym datasets. Code is available at https://github.com/jozhang97/MutateEverythingComment: NeurIPS 2023. Code available at https://github.com/jozhang97/MutateEverythin

Activated carbon as a carrier for amorphous drug delivery:effect of drug characteristics and carrier wettability

Recent research on porous silica materials as drug carriers for amorphous and controlled drug delivery has shown promising results. However, due to contradictory literature reports on toxicity and high costs of production, it is important to explore alternative safe and inexpensive porous carriers. In this study, the potential of activated carbon (AC) as an amorphous drug carrier was investigated using paracetamol (PA) and ibuprofen (IBU) as model drugs. The solution impregnation method was used for drug loading, with loading efficiency determined by UV spectroscopy and drug release kinetics studied using USP II dissolution apparatus. The physical state of the drug in the complex was characterised using differential scanning calorimetry and X-ray diffractions techniques, whilst sites of drug adsorption were studied using Fourier transform infrared spectroscopy and N2 adsorption techniques. In addition, the cytotoxicity of AC on human colon carcinoma (Caco-2) cells was assessed using the MTT assay. Results presented here reveal that, for PA/AC and IBU/AC complexes, the saturation solubility of the drug in the loading solvent appears to have an effect on the drug loading efficiency and the physical state of the drug loaded, whilst drug release kinetics were affected by the wettability of the activated carbon particles. Furthermore, activated carbon microparticles exhibited very low cytotoxicity on Caco-2 cells at the concentrations tested (10–800 μg/mL). This study, therefore, supports the potential of activated carbon as a carrier for amorphous drug delivery

Synthesis of Carbon Onion and Its Application as a Porous Carrier for Amorphous Drug Delivery

Given the great potential of porous carrier-based drug delivery for stabilising the amorphous form of drugs and enhancing dissolution profiles, this work is focussed on the synthesis and application of carbon onion or onion-like carbon (OLC) as a porous carrier for oral amorphous drug delivery, using paracetamol (PA) and ibuprofen (IBU) as model drugs. Annealing of nanodiamonds at 1100 °C produced OLC with a diamond core that exhibited low cytotoxicity on Caco-2 cells. Solution adsorption followed by centrifugation was used for drug loading and results indicated that the initial concentration of drug in the loading solution needs to be kept below 11.5% PA and 20.7% IBU to achieve complete amorphous loading. Also, no chemical interactions between the drug and OLC could be detected, indicating the safety of loading into OLC without changing the chemical nature of the drug. Drug release was complete in the presence of sodium dodecyl sulphate (SDS) and was faster compared to the pure crystalline drug, indicating the potential of OLC as an amorphous drug carrier

Phase Bubbles and Spatiotemporal Chaos in Granular Patterns

We use inelastic hard sphere molecular dynamics simulations and laboratory experiments to study patterns in vertically oscillated granular layers. The simulations and experiments reveal that {\em phase bubbles} spontaneously nucleate in the patterns when the container acceleration amplitude exceeds a critical value, about $7g$, where the pattern is approximately hexagonal, oscillating at one-fourth the driving frequency ($f/4$). A phase bubble is a localized region that oscillates with a phase opposite (differing by $\pi$) to that of the surrounding pattern; a localized phase shift is often called an {\em arching} in studies of two-dimensional systems. The simulations show that the formation of phase bubbles is triggered by undulation at the bottom of the layer on a large length scale compared to the wavelength of the pattern. Once formed, a phase bubble shrinks as if it had a surface tension, and disappears in tens to hundreds of cycles. We find that there is an oscillatory momentum transfer across a kink, and this shrinking is caused by a net collisional momentum inward across the boundary enclosing the bubble. At increasing acceleration amplitudes, the patterns evolve into randomly moving labyrinthian kinks (spatiotemporal chaos). We observe in the simulations that $f/3$ and $f/6$ subharmonic patterns emerge as primary instabilities, but that they are unstable to the undulation of the layer. Our experiments confirm the existence of transient $f/3$ and $f/6$ patterns.Comment: 6 pages, 12 figures, submitted to Phys. Rev. E on July 1st, 2001. for better quality figures, visit http://chaos.ph.utexas.edu/research/moo

Origin of multiplexing capabilities of multifrequency magnetic ratchets

Through a combination of theory, numerical simulation, and experiment, we investigate the motion of magnetic beads on the surface of a magnetic ratchet driven by multifrequency fields. Here, we focus on the influence of static forcing terms, which were not included in previous models, and we derive analytical models that show why the static forcing terms are responsible for inducing beads of two different sizes to move in opposite directions on the same ratchet potential. We begin our analysis with the simplest possible forcing model, and we show that the main effect of the static forcing terms is to delay the phase of flux reversal. From there, we move onto the full analysis and theoretically derive the phase range for which opposite motion among two different bead types is achieved. Based on these theoretical results, we conduct experimental investigations that explore the effects of bead size and static forcing coefficient on the direction of bead motion, which confirm most of the expected trends. These results shed light both on past experimental work both by ourselves and others, as well as elucidate the more general multiplexing capabilities of ratchets

Molecular spintronics: Coherent spin transfer in coupled quantum dots

Time-resolved Faraday rotation has recently demonstrated coherent transfer of electron spin between quantum dots coupled by conjugated molecules. Using a transfer Hamiltonian ansatz for the coupled quantum dots, we calculate the Faraday rotation signal as a function of the probe frequency in a pump-probe setup using neutral quantum dots. Additionally, we study the signal of one spin-polarized excess electron in the coupled dots. We show that, in both cases, the Faraday rotation angle is determined by the spin transfer probabilities and the Heisenberg spin exchange energy. By comparison of our results with experimental data, we find that the transfer matrix element for electrons in the conduction band is of order 0.08 eV and the spin transfer probabilities are of order 10%.Comment: 13 pages, 6 figures; minor change

Seebeck Effect in Magnetic Tunnel Junctions

Creating temperature gradients in magnetic nanostructures has resulted in a new research direction, i.e., the combination of magneto- and thermoelectric effects. Here, we demonstrate the observation of one important effect of this class: the magneto-Seebeck effect. It is observed when a magnetic configuration changes the charge based Seebeck coefficient. In particular, the Seebeck coefficient changes during the transition from a parallel to an antiparallel magnetic configuration in a tunnel junction. In that respect, it is the analog to the tunneling magnetoresistance. The Seebeck coefficients in parallel and antiparallel configuration are in the order of the voltages known from the charge-Seebeck effect. The size and sign of the effect can be controlled by the composition of the electrodes' atomic layers adjacent to the barrier and the temperature. Experimentally, we realized 8.8 % magneto-Seebeck effect, which results from a voltage change of about -8.7 {\mu}V/K from the antiparallel to the parallel direction close to the predicted value of -12.1 {\mu}V/K.Comment: 16 pages, 7 figures, 2 table

The secretion inhibitor Exo2 perturbs trafficking of Shiga toxin between endosomes and the trans-Golgi network

The small-molecule inhibitor Exo2 {4-hydroxy-3-methoxy-(5,6,7,8-tetrahydrol[1]benzothieno[2,3-d]pyrimidin-4-yl)hydraz-one benzaldehyde} has been reported to disrupt the Golgi apparatus completely and to stimulate Golgi–ER (endoplasmic reticulum) fusion in mammalian cells, akin to the well-characterized fungal toxin BFA (brefeldin A). It has also been reported that Exo2 does not affect the integrity of the TGN (trans-Golgi network), or the direct retrograde trafficking of the glycolipid-binding cholera toxin from the TGN to the ER lumen. We have examined the effects of BFA and Exo2, and found that both compounds are indistinguishable in their inhibition of anterograde transport and that both reagents significantly disrupt the morphology of the TGN in HeLa and in BS-C-1 cells. However, Exo2, unlike BFA, does not induce tubulation and merging of the TGN and endosomal compartments. Furthermore, and in contrast with its effects on cholera toxin, Exo2 significantly perturbs the delivery of Shiga toxin to the ER. Together, these results suggest that the likely target(s) of Exo2 operate at the level of the TGN, the Golgi and a subset of early endosomes, and thus Exo2 provides a more selective tool than BFA for examining membrane trafficking in mammalian cells

Towards an Explicit Model of D-brane Inflation

We present a detailed analysis of an explicit model of warped D-brane inflation, incorporating the effects of moduli stabilization. We consider the potential for D3-brane motion in a warped conifold background that includes fluxes and holomorphically-embedded D7-branes involved in moduli stabilization. Although the D7-branes significantly modify the inflaton potential, they do not correct the quadratic term in the potential, and hence do not cause a uniform change in the slow-roll parameter eta. Nevertheless, we present a simple example based on the Kuperstein embedding of D7-branes, z_1=constant, in which the potential can be fine-tuned to be sufficiently flat for inflation. To derive this result, it is essential to incorporate the fact that the compactification volume changes slightly as the D3-brane moves. We stress that the compactification geometry dictates certain relationships among the parameters in the inflaton Lagrangian, and these microscopic constraints impose severe restrictions on the space of possible models. We note that the shape of the final inflaton potential differs from projections given in earlier studies: in configurations where inflation occurs, it does so near an inflection point. Finally, we comment on the difficulty of making precise cosmological predictions in this scenario. This is the companion paper to arXiv:0705.3837.Comment: 68 pages, 6 figures; v2: fixed typos, added refs and clarifications; v3: expanded discussion of inflection point inflatio

Patient-reported symptom burden of Charcot-Marie-Tooth Disease Type 1A: findings from an observational digital lifestyle study

Objectives: This study aims to explore the impact of Charcot-Marie-Tooth disease type 1A (CMT1A) and its treatment on patients in European (France, Germany, Italy, Spain, and the United Kingdom) and US real-world practice. Methods: Adults with CMT1A (n = 937) were recruited to an ongoing observational study exploring the impact of CMT. Data were collected via CMT&Me, an app through which participants completed patient-reported outcome measures. Results: Symptoms ranked with highest importance were weakness in the extremities, difficulty in walking, and fatigue. Almost half of participants experienced a worsening of symptom severity since diagnosis. Anxiety and depression were each reported by over one-third of participants. Use of rehabilitative interventions, medications, and orthotics/walking aids was high. Conclusions: Patient-reported burden of CMT1A is high, influenced by difficulties in using limbs, fatigue, pain, and impaired quality of life. Burden severity appears to differ across the population, possibly driven by differences in rehabilitative and prescription-based interventions, and country-specific health care variability