Multi-qubit entanglement and algorithms on a neutral-atom quantum computer.

Gate-model quantum computers promise to solve currently intractable computational problems if they can be operated at scale with long coherence times and high-fidelity logic. Neutral-atom hyperfine qubits provide inherent scalability owing to their identical characteristics, long coherence times and ability to be trapped in dense, multidimensional arrays1. Combined with the strong entangling interactions provided by Rydberg states2-4, all the necessary characteristics for quantum computation are available. Here we demonstrate several quantum algorithms on a programmable gate-model neutral-atom quantum computer in an architecture based on individual addressing of single atoms with tightly focused optical beams scanned across a two-dimensional array of qubits. Preparation of entangled Greenberger-Horne-Zeilinger (GHZ) states5 with up to six qubits, quantum phase estimation for a chemistry problem6 and the quantum approximate optimization algorithm (QAOA)7 for the maximum cut (MaxCut) graph problem are demonstrated. These results highlight the emergent capability of neutral-atom qubit arrays for universal, programmable quantum computation, as well as preparation of non-classical states of use for quantum-enhanced sensing.

A universal 3D imaging sensor on a silicon photonics platform.

Accurate three-dimensional (3D) imaging is essential for machines to map and interact with the physical world1,2. Although numerous 3D imaging technologies exist, each addressing niche applications with varying degrees of success, none has achieved the breadth of applicability and impact that digital image sensors have in the two-dimensional imaging world3-10. A large-scale two-dimensional array of coherent detector pixels operating as a light detection and ranging system could serve as a universal 3D imaging platform. Such a system would offer high depth accuracy and immunity to interference from sunlight, as well as the ability to measure the velocity of moving objects directly11. Owing to difficulties in providing electrical and photonic connections to every pixel, previous systems have been restricted to fewer than 20 pixels12-15. Here we demonstrate the operation of a large-scale coherent detector array, consisting of 512 pixels, in a 3D imaging system. Leveraging recent advances in the monolithic integration of photonic and electronic circuits, a dense array of optical heterodyne detectors is combined with an integrated electronic readout architecture, enabling straightforward scaling to arbitrarily large arrays. Two-axis solid-state beam steering eliminates any trade-off between field of view and range. Operating at the quantum noise limit16,17, our system achieves an accuracy of 3.1 millimetres at a distance of 75 metres when using only 4 milliwatts of light, an order of magnitude more accurate than existing solid-state systems at such ranges. Future reductions of pixel size using state-of-the-art components could yield resolutions in excess of 20 megapixels for arrays the size of a consumer camera sensor. This result paves the way for the development and proliferation of low-cost, compact and high-performance 3D imaging cameras that could be used in applications from robotics and autonomous navigation to augmented reality and healthcare.

A guide to the visual analysis and communication of biomolecular structural data.

Biologists regularly face an increasingly difficult task - to effectively communicate bigger and more complex structural data using an ever-expanding suite of visualization tools. Whether presenting results to peers or educating an outreach audience, a scientist can achieve maximal impact with minimal production time by systematically identifying an audience's needs, planning solutions from a variety of visual communication techniques and then applying the most appropriate software tools. A guide to available resources that range from software tools to professional illustrators can help researchers to generate better figures and presentations tailored to any audience's needs, and enable artistically inclined scientists to create captivating outreach imagery.

Tafasitamab and lenalidomide in large B-cell lymphoma: real-world outcomes in a multicenter retrospective study.

ABSTRACT: In this real-world evaluation of tafasitamab-lenalidomide (TL) in relapsed or refractory LBCL, patients receiving TL had higher rates of comorbidities and high-risk disease characteristics, and substantially lower progression-free survival and overall survival, compared with the L-MIND registration clinical trial for TL.

Longitudinal Associations between Homelessness and Substance Use: Investigating Demographic Differences for Young Adults in Treatment.

Objective: To examine prospective, bidirectional associations between homelessness and substance use frequency among young adults receiving substance use treatment in the United States. We also investigated potential differences across demographic subgroups. Methods: Young adults (N = 3717, Mage = 20.1, 28% female, 7.3% sexual/gender minority, and 37% non-Hispanic White) receiving substance use treatment in the U.S. completed assessments at intake, 3 months, 6 months, and 12 months post-intake. Latent growth curve models with structured residuals (LGC-SR) were used to examine cross-lagged associations between homeless days and frequency of substance use and associated problems. Models were stratified by sex, race/ethnicity, and sexual and/or gender minority status. Results: Overall, days spent homeless (µslope= -0.19, p = 0.046) and substance use frequency (µslope1= -6.19, p < 0.001) significantly decreased during treatment, with no significant cross-lagged associations between homeless days and substance use frequency. However, results differed by race and ethnicity. For non-Hispanic White young adults, greater substance use at treatment entry was associated with steeper declines in homeless days between-persons (ϕstandardized = -0.14, p = 0.04). For African Americans, homeless days at treatment entry were associated with greater increases in substance use between-persons (ϕstandardized = 0.29, p = 0.04). No significant differences were found by sex or sexual/gender minority status. Conclusions: Despite overall declines in homelessness and substance use during treatment, these outcomes may unfold differently for non-Hispanic White and African American young adults. More support may be needed for African American young adults reporting homelessness at treatment entry.

International Medical Graduates and the Physician Workforce.

Importance: Physician shortages and the geographic maldistribution of general and specialist physicians impair health care delivery and worsen health inequity in the US. International medical graduates (IMGs) represent a potential solution given their ready supply. Observations: Despite extensive clinical experience, evidence of competence, and willingness to practice in underserved communities, IMGs experience multiple barriers to entry in the US, including the immigration process, the pathways available for certification and licensing, and institutional reluctance to consider non-US-trained candidates. International medical graduates applying to postgraduate training programs compare favorably with US-trained candidates in terms of clinical experience, prior formal postgraduate training, and research, but have higher application withdrawal rates and significantly lower residency and fellowship match rates, a disparity that may be exacerbated by the recent elimination of objective performance metrics, such as the US Medical Licensing Examination Step 1 score. Once legally in the US, IMGs encounter additional obstacles to board eligibility, research funding, and career progression. Conclusions and Relevance: International medical graduates offer a viable and available solution to bridge the domestic physician supply gap, while improving workforce diversity and meaningfully addressing the public health implications of geographic maldistribution of general and specialist physicians, without disrupting existing physician stature and salaries. The US remains unable to integrate IMGs until systematic policy changes at the national level are implemented.

The Potential of NIR Spectroscopy and Chemometrics to Discriminate Roast Degrees and Predict Volatiles in Coffee.

This study aimed to establish a rapid and practical method for monitoring and predicting volatile compounds during coffee roasting using near-infrared (NIR) spectroscopy coupled with chemometrics. Washed Arabica coffee beans from Ethiopia and Congo were roasted to industry-validated light, medium, and dark degrees. Concurrent analysis of the samples was performed using gas chromatography-mass spectrometry (GC-MS) and NIR spectroscopy, generating datasets for partial least squares (PLS) regression analysis. The results showed that NIR spectroscopy successfully differentiated the differently roasted samples, similar to the discrimination achieved by GC-MS. This finding highlights the potential of NIR spectroscopy as a rapid tool for monitoring and standardizing the degree of coffee roasting in the industry. A PLS regression model was developed using Ethiopian samples to explore the feasibility of NIR spectroscopy to indirectly measure the volatiles that are important in classifying the roast degree. For PLSR, the data underwent autoscaling as a preprocessing step, and the optimal number of latent variables (LVs) was determined through cross-validation, utilizing the root mean squared error (RMSE). The model was further validated using Congo samples and successfully predicted (with R2 values > 0.75 and low error) over 20 volatile compounds, including furans, ketones, phenols, and pyridines. Overall, this study demonstrates the potential of NIR spectroscopy as a practical and rapid method to complement current techniques for monitoring and predicting volatile compounds during the coffee roasting process.

Building the next generation of virtual cells to understand cellular biology.

Cell science has made significant progress by focusing on understanding individual cellular processes through reductionist approaches. However, the sheer volume of knowledge collected presents challenges in integrating this information across different scales of space and time to comprehend cellular behaviors, as well as making the data and methods more accessible for the community to tackle complex biological questions. This perspective proposes the creation of next-generation virtual cells, which are dynamic 3D models that integrate information from diverse sources, including simulations, biophysical models, image-based models, and evidence-based knowledge graphs. These virtual cells would provide statistically accurate and holistic views of real cells, bridging the gap between theoretical concepts and experimental data, and facilitating productive new collaborations among researchers across related fields.

High-speed 4 × 4 silicon photonic plasma dispersive switch, operating at the 2†µm waveband.

The escalating need for expansive data bandwidth, and the resulting capacity constraints of the single mode fiber (SMF) have positioned the 2-µm waveband as a prospective window for emerging applications in optical communication. This has initiated an ecosystem of silicon photonic components in the region driven by CMOS compatibility, low cost, high efficiency and potential for large-scale integration. In this study, we demonstrate a plasma dispersive 4 × 4 photonic switch operating at the 2-µm waveband with the highest switching speed. The demonstrated switch operates across a 45-nm bandwidth, with 10-90% rise and 90-10% fall time of 1.78 ns and 3.02 ns respectively. In a 4 × 4 implementation, crosstalk below -15 dB and power consumption lower than 19.15 mW across all 16 optical paths are indicated. This result brings high-speed optical switching to the portfolio of devices at the promising waveband.

Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus.

Antimicrobial resistance presents a significant health care crisis. The mutation F98Y in Staphylococcus aureus dihydrofolate reductase (SaDHFR) confers resistance to the clinically important antifolate trimethoprim (TMP). Propargyl-linked antifolates (PLAs), next generation DHFR inhibitors, are much more resilient than TMP against this F98Y variant, yet this F98Y substitution still reduces efficacy of these agents. Surprisingly, differences in the enantiomeric configuration at the stereogenic center of PLAs influence the isomeric state of the NADPH cofactor. To understand the molecular basis of F98Y-mediated resistance and how PLAs' inhibition drives NADPH isomeric states, we used protein design algorithms in the osprey protein design software suite to analyze a comprehensive suite of structural, biophysical, biochemical, and computational data. Here, we present a model showing how F98Y SaDHFR exploits a different anomeric configuration of NADPH to evade certain PLAs' inhibition, while other PLAs remain unaffected by this resistance mechanism.

Multiscale architecture for fast optical addressing and control of large-scale qubit arrays.

This paper presents a technique for rapid site-selective control of the quantum state of particles in a large array using the combination of a fast deflector (e.g., an acousto-optic deflector) and a relatively slow spatial light modulator (SLM). The use of SLMs for site-selective quantum state manipulation has been limited due to slow transition times that prevent rapid, consecutive quantum gates. By partitioning the SLM into multiple segments and using a fast deflector to transition between them, it is possible to substantially reduce the average time increment between scanner transitions by increasing the number of gates that can be performed for a single SLM full-frame setting. We analyzed the performance of this device in two different configurations: In configuration 1, each SLM segment addresses the full qubit array; in configuration 2, each SLM segment addresses a subarray and an additional fast deflector positions that subarray with respect to the full qubit array. With these hybrid scanners, we calculated qubit addressing rates that are tens to hundreds of times faster than using an SLM alone.

Health Status, Persistent Symptoms, and Effort Intolerance One Year After Acute COVID-19 Infection.

BACKGROUND: The long-term prevalence and risk factors for post-acute COVID-19 sequelae (PASC) are not well described and may have important implications for unvaccinated populations and policy makers. OBJECTIVE: To assess health status, persistent symptoms, and effort tolerance approximately 1 year after COVID-19 infection DESIGN: Retrospective observational cohort study using surveys and clinical data PARTICIPANTS: Survey respondents who were survivors of acute COVID-19 infection requiring Emergency Department presentation or hospitalization between March 3 and May 15, 2020. MAIN MEASURE(S): Self-reported health status, persistent symptoms, and effort tolerance KEY RESULTS: The 530 respondents (median time between hospital presentation and survey 332 days [IQR 325-344]) had mean age 59.2±16.3 years, 44.5% were female and 70.8% were non-White. Of these, 41.5% reported worse health compared to a year prior, 44.2% reported persistent symptoms, 36.2% reported limitations in lifting/carrying groceries, 35.5% reported limitations climbing one flight of stairs, 38.1% reported limitations bending/kneeling/stooping, and 22.1% reported limitations walking one block. Even those without high-risk comorbid conditions and those seen only in the Emergency Department (but not hospitalized) experienced significant deterioration in health, persistent symptoms, and limitations in effort tolerance. Women (adjusted relative risk ratio [aRRR] 1.26, 95% CI 1.01-1.56), those requiring mechanical ventilation (aRRR 1.48, 1.02-2.14), and people with HIV (aRRR 1.75, 1.14-2.69) were significantly more likely to report persistent symptoms. Age and other risk factors for more severe COVID-19 illness were not associated with increased risk of PASC. CONCLUSIONS: PASC may be extraordinarily common 1 year after COVID-19, and these symptoms are sufficiently severe to impact the daily exercise tolerance of patients. PASC symptoms are broadly distributed, are not limited to one specific patient group, and appear to be unrelated to age. These data have implications for vaccine hesitant individuals, policy makers, and physicians managing the emerging longer-term yet unknown impact of the COVID-19 pandemic.

Suppression of Kv3.3 channels by antisense oligonucleotides reverses biochemical effects and motor impairment in spinocerebellar ataxia type 13 mice.

Mutations in KCNC3, the gene that encodes the Kv3.3 voltage dependent potassium channel, cause Spinocerebellar Ataxia type 13 (SCA13), a disease associated with disrupted motor behaviors, progressive cerebellar degeneration, and abnormal auditory processing. The Kv3.3 channel directly binds Hax-1, a cell survival protein. A disease-causing mutation, Kv3.3-G592R, causes overstimulation of Tank Binding Kinase 1 (Tbk1) in the cerebellum, resulting in the degradation of Hax-1 by promoting its trafficking into multivesicular bodies and then to lysosomes. We have now tested the effects of antisense oligonucleotides (ASOs) directed against the Kv3.3 channel on both wild type mice and those bearing the Kv3.3-G592R-encoding mutation. Intracerebroventricular infusion of the Kcnc3-specific ASO suppressed both mRNA and protein levels of the Kv3.3 channel. In wild-type animals, this produced no change in levels of activated Tbk1, Hax-1 or Cd63, a tetraspanin marker for late endosomes/multivesicular bodies. In contrast, in mice homozygous for the Kv3.3-G592R-encoding mutation, the same ASO reduced Tbk1 activation and levels of Cd63, while restoring the expression of Hax-1 in the cerebellum. The motor behavior of the mice was tested using a rotarod assay. Surprisingly, the active ASO had no effects on the motor behavior of wild type mice but restored the behavior of the mutant mice to those of age-matched wild type animals. Our findings indicate that, in mature intact animals, suppression of Kv3.3 expression can reverse the deleterious effects of a SCA13 mutation while having little effect on wild type animals. Thus, targeting Kv3.3 expression may prove a viable therapeutic approach for SCA13.

A novel cell line panel reveals non-genetic mediators of platinum resistance and phenotypic diversity in high grade serous ovarian cancer.

OBJECTIVES: Resistance to cancer therapy is an enduring challenge and accurate and reliable preclinical models are lacking. We interrogated this unmet need using high grade serous ovarian cancer (HGSC) as a disease model. METHODS: We created five in vitro and two in vivo platinum-resistant HGSC models and characterised the entire cell panel via whole genome sequencing, RNASeq and creation of intraperitoneal models. RESULTS: Mutational signature analysis indicated that platinum-resistant cell lines evolved from a pre-existing ancestral clone but a unifying mutational cause for drug resistance was not identified. However, cisplatin-resistant and carboplatin-resistant cells evolved recurrent changes in gene expression that significantly overlapped with independent samples obtained from multiple patients with relapsed HGSC. Gene Ontology Biological Pathways (GOBP) related to the tumour microenvironment, particularly the extracellular matrix, were repeatedly enriched in cisplatin-resistant cells, carboplatin-resistant cells and also in human resistant/refractory samples. The majority of significantly over-represented GOBP however, evolved uniquely in either cisplatin- or carboplatin-resistant cell lines resulting in diverse intraperitoneal behaviours that reflect different clinical manifestations of relapsed human HGSC. CONCLUSIONS: Our clinically relevant and usable models reveal a key role for non-genetic factors in the evolution of chemotherapy resistance. Biological pathways relevant to the extracellular matrix were repeatedly expressed by resistant cancer cells in multiple settings. This suggests that recurrent gene expression changes provide a fitness advantage during platinum therapy and also that cancer cell-intrinsic mechanisms influence the tumour microenvironment during the evolution of drug resistance. Candidate genes and pathways identified here could reveal therapeutic opportunities in platinum-resistant HGSC.

Factors Affecting Slip Progression After In Situ Screw Fixation of Stable Slipped Capital Femoral Epiphysis.

BACKGROUND: Slip progression after in situ fixation of slipped capital femoral epiphysis (SCFE) has been reported as occurring in up to 20% of patients. We review SCFE treated with in situ single screw fixation performed at 2 hospitals over a 15-year period to determine the factors associated with slip progression. METHODS: This case-control study reviews SCFE treated with in situ single cannulated screw fixation with minimum follow up of 1 year and full closure of the affected physis. Slip progression (failure) was defined as worsening of the Southwick slip angle of 10 or more degrees or revision surgery for symptomatic slip progression. Univariate and multivariate analyses were performed comparing success and failure groups for patient characteristics, screw type and position, and radiographic measurements. RESULTS: Ninety three patients with 108 slips met all criteria, with 15 hips (14%) classified as having slip progression (failure). All failures had 3 threads or fewer across the physis. Five hips had 2 threads across the physis, and 4 of the 5 were classified as failures. Lower modified Oxford bone scores were found in the failure group, though the difference was small (0.9, P=0.013). Failure was also associated with partially threaded screws (P=0.001). Failed hips were associated with lower initial Southwick angles (32.8 degrees) than successful hips (40.4 degrees) (P=0.047). In the stepwise model for multivariate regression, 4 factors were identified as significant, with lower initial number of threads (P<0.0001), mild initial Southwick category (P=0.0050), male sex (P=0.0061), and partially threaded screw type (P=0.0116) predicting failure. CONCLUSION: This study is the largest to date evaluating risk factors for slip progression after SCFE fixation, and the first to consider revision surgery for symptomatic slip progression. For stable SCFE, we demonstrate that 4 threads across the physis with a fully threaded screw of 6.5 mm diameter or greater was sufficient to avoid slip progression. We provide a risk stratification for progression of slip showing that in some cases 3 threads across the physis may be sufficient. LEVEL OF EVIDENCE: Level III-case-control study.

Near-IR & Mid-IR Silicon Photonics Modulators.

As the silicon photonics field matures and a data-hungry future looms ahead, new technologies are required to keep up pace with the increase in capacity demand. In this paper, we review current developments in the near-IR and mid-IR group IV photonic modulators that show promising performance. We analyse recent trends in optical and electrical co-integration of modulators and drivers enabling modulation data rates of 112 GBaud in the near infrared. We then describe new developments in short wave infrared spectrum modulators such as employing more spectrally efficient PAM-4 coding schemes for modulations up to 40 GBaud. Finally, we review recent results at the mid infrared spectrum and application of the thermo-optic effect for modulation as well as the emergence of new platforms based on germanium to tackle the challenges of modulating light in the long wave infrared spectrum up to 10.7 µm with data rates of 225 MBaud.

The budding yeast transition to quiescence.

A subset of Saccharomyces cerevisiae cells in a stationary phase culture achieve a unique quiescent state characterized by increased cell density, stress tolerance, and longevity. Trehalose accumulation is necessary but not sufficient for conferring this state, and it is not recapitulated by abrupt starvation. The fraction of cells that achieve this state varies widely in haploids and diploids and can approach 100%, indicating that both mother and daughter cells can enter quiescence. The transition begins when about half the glucose has been taken up from the medium. The high affinity glucose transporters are turned on, glycogen storage begins, the Rim15 kinase enters the nucleus and the accumulation of cells in G1 is initiated. After the diauxic shift (DS), when glucose is exhausted from the medium, growth promoting genes are repressed by the recruitment of the histone deacetylase Rpd3 by quiescence-specific repressors. The final division that takes place post-DS is highly asymmetrical and G1 arrest is complete after 48 h. The timing of these events can vary considerably, but they are tightly correlated with total biomass of the culture, suggesting that the transition to quiescence is tightly linked to changes in external glucose levels. After 7 days in culture, there are massive morphological changes at the protein and organelle level. There are global changes in histone modification. An extensive array of condensin-dependent, long-range chromatin interactions lead to genome-wide chromatin compaction that is conserved in yeast and human cells. These interactions are required for the global transcriptional repression that occurs in quiescent yeast.

High-speed silicon Michelson interferometer modulator and streamlined IMDD PAM-4 transmission of Mach-Zehnder modulators for the 2 µm wavelength band.

We demonstrate high-speed silicon modulators optimized for operating at the wavelength of 2 µm. The Mach-Zehnder interferometer (MZI) carrier-depletion modulator with 2 mm phase shifter has a single-arm modulation efficiency (Vπ ·Lπ) of 2.89 V·cm at 4 V reverse bias. Using a push-pull configuration it operates at a data rate of 25 Gbit/s OOK with an extinction ratio of 6.25 dB. We also proposed a mathematically-analysed streamlined IMDD PAM-4 scheme and successfully demonstrated a 25 Gbit/s datarate PAM-4 with the same 2 mm modulator. A Michelson interferometer carrier-depletion modulator with 0.5 mm phase shift length has also been shown with modulation efficiency (Vπ ·Lπ) of 1.36 V·cm at 4 V reverse bias and data rate of 20 Gbit/s OOK. The Michelson interferometer modulator performs similarly to a Mach-Zehnder modulator with twice the phase shifter length.

Thirty-Day Post-Discharge Outcomes Following COVID-19 Infection.

BACKGROUND: The clinical course of COVID-19 includes multiple disease phases. Data describing post-hospital discharge outcomes may provide insight into disease course. Studies describing post-hospitalization outcomes of adults following COVID-19 infection are limited to electronic medical record review, which may underestimate the incidence of outcomes. OBJECTIVE: To determine 30-day post-hospitalization outcomes following COVID-19 infection. DESIGN: Retrospective cohort study SETTING: Quaternary referral hospital and community hospital in New York City. PARTICIPANTS: COVID-19 infected patients discharged alive from the emergency department (ED) or hospital between March 3 and May 15, 2020. MEASUREMENT: Outcomes included return to an ED, re-hospitalization, and mortality within 30 days of hospital discharge. RESULTS: Thirty-day follow-up data were successfully collected on 94.6% of eligible patients. Among 1344 patients, 16.5% returned to an ED, 9.8% were re-hospitalized, and 2.4% died. Among patients who returned to the ED, 50.0% (108/216) went to a different hospital from the hospital of the index presentation, and 61.1% (132/216) of those who returned were re-hospitalized. In Cox models adjusted for variables selected using the lasso method, age (HR 1.01 per year [95% CI 1.00-1.02]), diabetes (1.54 [1.06-2.23]), and the need for inpatient dialysis (3.78 [2.23-6.43]) during the index presentation were independently associated with a higher re-hospitalization rate. Older age (HR 1.08 [1.05-1.11]) and Asian race (2.89 [1.27-6.61]) were significantly associated with mortality. CONCLUSIONS: Among patients discharged alive following their index presentation for COVID-19, risk for returning to a hospital within 30 days of discharge was substantial. These patients merit close post-discharge follow-up to optimize outcomes.

Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface.

The K* algorithm provably approximates partition functions for a set of states (e.g., protein, ligand, and protein-ligand complex) to a user-specified accuracy ε. Often, reaching an ε-approximation for a particular set of partition functions takes a prohibitive amount of time and space. To alleviate some of this cost, we introduce two new algorithms into the osprey suite for protein design: fries, a Fast Removal of Inadequately Energied Sequences, and EWAK*, an Energy Window Approximation to K*. fries pre-processes the sequence space to limit a design to only the most stable, energetically favorable sequence possibilities. EWAK* then takes this pruned sequence space as input and, using a user-specified energy window, calculates K* scores using the lowest energy conformations. We expect fries/EWAK* to be most useful in cases where there are many unstable sequences in the design sequence space and when users are satisfied with enumerating the low-energy ensemble of conformations. In combination, these algorithms provably retain calculational accuracy while limiting the input sequence space and the conformations included in each partition function calculation to only the most energetically favorable, effectively reducing runtime while still enriching for desirable sequences. This combined approach led to significant speed-ups compared to the previous state-of-the-art multi-sequence algorithm, BBK*, while maintaining its efficiency and accuracy, which we show across 40 different protein systems and a total of 2,826 protein design problems. Additionally, as a proof of concept, we used these new algorithms to redesign the protein-protein interface (PPI) of the c-Raf-RBD:KRas complex. The Ras-binding domain of the protein kinase c-Raf (c-Raf-RBD) is the tightest known binder of KRas, a protein implicated in difficult-to-treat cancers. fries/EWAK* accurately retrospectively predicted the effect of 41 different sets of mutations in the PPI of the c-Raf-RBD:KRas complex. Notably, these mutations include mutations whose effect had previously been incorrectly predicted using other computational methods. Next, we used fries/EWAK* for prospective design and discovered a novel point mutation that improves binding of c-Raf-RBD to KRas in its active, GTP-bound state (KRasGTP). We combined this new mutation with two previously reported mutations (which were highly-ranked by osprey) to create a new variant of c-Raf-RBD, c-Raf-RBD(RKY). fries/EWAK* in osprey computationally predicted that this new variant binds even more tightly than the previous best-binding variant, c-Raf-RBD(RK). We measured the binding affinity of c-Raf-RBD(RKY) using a bio-layer interferometry (BLI) assay, and found that this new variant exhibits single-digit nanomolar affinity for KRasGTP, confirming the computational predictions made with fries/EWAK*. This new variant binds roughly five times more tightly than the previous best known binder and roughly 36 times more tightly than the design starting point (wild-type c-Raf-RBD). This study steps through the advancement and development of computational protein design by presenting theory, new algorithms, accurate retrospective designs, new prospective designs, and biochemical validation.