Synthetic molecular machines for active self-assembly : prototype algorithms, designs, and experimental study

Computer science and electrical engineering have been the great success story of the twentieth century. The neat modularity and mapping of a language onto circuits has led to robots on Mars, desktop computers and smartphones. But these devices are not yet able to do some of the things that life takes for granted: repair a scratch, reproduce, regenerate, or grow exponentially fast–all while remaining functional.

This thesis explores and develops algorithms, molecular implementations, and theoretical proofs in the context of “active self-assembly” of molecular systems. The long-term vision of active self-assembly is the theoretical and physical implementation of materials that are composed of reconfigurable units with the programmability and adaptability of biology’s numerous molecular machines. En route to this goal, we must first find a way to overcome the memory limitations of molecular systems, and to discover the limits of complexity that can be achieved with individual molecules.

One of the main thrusts in molecular programming is to use computer science as a tool for figuring out what can be achieved. While molecular systems that are Turing-complete have been demonstrated [Winfree, 1996], these systems still cannot achieve some of the feats biology has achieved.

One might think that because a system is Turing-complete, capable of computing “anything,” that it can do any arbitrary task. But while it can simulate any digital computational problem, there are many behaviors that are not “computations” in a classical sense, and cannot be directly implemented. Examples include exponential growth and molecular motion relative to a surface.

Passive self-assembly systems cannot implement these behaviors because (a) molecular motion relative to a surface requires a source of fuel that is external to the system, and (b) passive systems are too slow to assemble exponentially-fast-growing structures. We call these behaviors “energetically incomplete” programmable behaviors. This class of behaviors includes any behavior where a passive physical system simply does not have enough physical energy to perform the specified tasks in the requisite amount of time.

As we will demonstrate and prove, a sufficiently expressive implementation of an “active” molecular self-assembly approach can achieve these behaviors. Using an external source of fuel solves part of the the problem, so the system is not “energetically incomplete.” But the programmable system also needs to have sufficient expressive power to achieve the specified behaviors. Perhaps surprisingly, some of these systems do not even require Turing completeness to be sufficiently expressive.

Building on a large variety of work by other scientists in the fields of DNA nanotechnology, chemistry and reconfigurable robotics, this thesis introduces several research contributions in the context of active self-assembly.

We show that simple primitives such as insertion and deletion are able to generate complex and interesting results such as the growth of a linear polymer in logarithmic time and the ability of a linear polymer to treadmill. To this end we developed a formal model for active-self assembly that is directly implementable with DNA molecules. We show that this model is computationally equivalent to a machine capable of producing strings that are stronger than regular languages and, at most, as strong as context-free grammars. This is a great advance in the theory of active self- assembly as prior models were either entirely theoretical or only implementable in the context of macro-scale robotics.

We developed a chain reaction method for the autonomous exponential growth of a linear DNA polymer. Our method is based on the insertion of molecules into the assembly, which generates two new insertion sites for every initial one employed. The building of a line in logarithmic time is a first step toward building a shape in logarithmic time. We demonstrate the first construction of a synthetic linear polymer that grows exponentially fast via insertion. We show that monomer molecules are converted into the polymer in logarithmic time via spectrofluorimetry and gel electrophoresis experiments. We also demonstrate the division of these polymers via the addition of a single DNA complex that competes with the insertion mechanism. This shows the growth of a population of polymers in logarithmic time. We characterize the DNA insertion mechanism that we utilize in Chapter 4. We experimentally demonstrate that we can control the kinetics of this re- action over at least seven orders of magnitude, by programming the sequences of DNA that initiate the reaction.

In addition, we review co-authored work on programming molecular robots using prescriptive landscapes of DNA origami; this was the first microscopic demonstration of programming a molec- ular robot to walk on a 2-dimensional surface. We developed a snapshot method for imaging these random walking molecular robots and a CAPTCHA-like analysis method for difficult-to-interpret imaging data.

Alterações eritrocitárias induzidas pelo exercício físico

Evidências crescentes têm demonstrado que o exercício prejudica a estrutura da membrana eritrocitária, como consequência do aumento do estresse físico e químico. O óxido nítrico (NO) derivado dos eritrócitos afeta a fluidez da membrana e a sua biodisponibilidade depende do equilíbrio entre a sua síntese e eliminação por espécies reativas de oxigênio. Nós investigamos se o exercício realizado em diferentes intensidades afetaria biodisponibilidade do NO eritrocitário e se levaria a um quadro de estresse oxidativo. Dez homens (26 4 anos, VO2pico 44,1 4,3 mL.kg-1.min-1) realizaram um teste cardiopulmonar máximo em esteira e um teste de exercício submáximo a 70% VO2pico durante 30 min. O sangue foi coletado em repouso e imediatamente após os exercícios para isolamento dos eritrócitos. O exercício máximo aumentou a contagem de eritrócitos, hemoglobina e hematócrito, sem levar a qualquer alteração na massa corporal que pudesse sugerir hemoconcentração devido a uma redução do volume plasmático. Observou-se uma diminuição do influxo de L-arginina depois do teste submáximo, mas não no teste máximo. No entanto, a atividade da óxido nítrico sintase, ou seja, a produção de NO, foi aumentada após o teste máximo. Os níveis de GMPc não se alteraram após ambos os teste de exercício. Em relação aos biomarcadores de estresse oxidativo, o exercício submáximo reduziu a oxidação proteica e aumentou a atividade da catalase e a expressão da glutationa peroxidase, enquanto que o exercício máximo levou a uma maior peroxidação lipídica e diminuição da atividade da SOD. Nem a atividade glutationa peroxidase ou a expressão NADPH oxidase foram afetadas pelo exercício. Estes resultados sugerem que o exercício induziu alterações no estresse oxidativo de eritrócitos, que parecem estar mais associadas com a intensidade do que a duração do execicio. Além disso, nas intensidades recomendadas para a promoção da saúde, o exercício mostrou ser protetor, aumentando a atividade e a expressão de enzimas antioxidantes importantes e reduzindo os danos oxidativos.

Comparação das variáveis fisiológicas e psicológicas em diferentes configurações de exercícios aeróbios

Existem diversas recomendações de treinamento aeróbio. Contudo, exercícios auto-ajustados têm sido indicados sob a premissa de gerar melhor resposta afetiva (ex.: prazer) gerando possivelmente maior chance de adesão. Diante da baixa adesão ao exercício e considerando seus benefícios, é necessário verificar que atividade gera melhor resposta afetiva. Esta dissertação investiga esta questão e é composta por dois estudos. Comparar as respostas fisiológicas e afetivas geradas por duas recomendações de treinamento aeróbio. Vinte e quatro participantes realizaram 3 sessões em esteira rolante. Foram determinados o nível de atividade física (questionário IPAQ) e o VO2Max. Nas visitas 2 e 3 foram aplicadas as recomendações aeróbias, uma baseada no nível de atividade física (PBPA) e outra baseada no VO2Max (PBVO2Max). Os dados foram divididos em quartis (Q). A PBPA gerou risco 150% maior de abandono da sessão de treino. O tamanho do efeito (TE) mostrou maior resposta afetiva (escala de sensações) para a PBVO2Max no Q4 (TE 0,41) e menor FC na PBVO2Max (TE médio dos quartis -0,85). Comparar as respostas fisiológicas e afetivas de atividades impostas e auto-ajustadas. Catorze participantes realizaram 3 sessões em cicloergômetro. O VO2Max foi determinado na visita 1. Na visita 2 foi realizada uma atividade AA e na visita 3 uma atividade imposta. Não foram encontradas diferenças significativas entre as atividades AA e imposta nas variáveis fisiológicas (FC, VO2, e lactato; p>0,05), na potência (p>0,05) e nas variáveis perceptivas (esforço percebido, escala de sensações e escala de ativação; p>0,05). Prescrições baseadas no VO2Max parecem proporcionar melhor resposta afetiva. O tipo de prescrição realizada (auto-ajustada ou imposta) parece não influenciar a resposta afetiva dos indivíduos. Os achados sugerem que um ajuste adequado do treino pode gerar melhores respostas afetivas

Step synchronization and third person speed perception in virtual environment locomotion simulators

Human locomotion is known to be influenced by observation of another person's gait. For example, athletes often synchronize their step in long distance races. However, how interaction with a virtual runner affects the gait of a real runner has not been studied. We investigated this by creating an illusion of running behind a virtual model (VM) using a treadmill and large screen virtual environment showing a video of a VM. We looked at step synchronization between the real and virtual runner and at the role of the step frequency (SF) in the real runner's perception of VM speed. We found that subjects match VM SF when asked to match VM speed with their own (Figure 1). This indicates step synchronization may be a strategy of speed matching or speed perception. Subjects chose higher speeds when VMSF was higher (though VM was 12km/h in all videos). This effect was more pronounced when the speed estimate was rated verbally while standing still. (Figure 2). This may due to correlated physical activity affecting the perception of VM speed [Jacobs et al. 2005]; or step synchronization altering the subjects' perception of self speed [Durgin et al. 2007]. Our findings indicate that third person activity in a collaborative virtual locomotive environment can have a pronounced effect on an observer's gait activity and their perceptual judgments of the activity of others: the SF of others (virtual or real) can potentially influence one's perception of self speed and lead to changes in speed and SF. A better understanding of the underlying mechanisms would support the design of more compelling virtual trainers and may be instructive for competitive athletics in the real world. © 2009 ACM.

Development and validation of a sport-specific exercise protocol for elite youth soccer players

Thatcher, Rhys, and Alan Batterham, 'Development and validation of a sport-specific exercise protocol for elite youth soccer players', Journal of Sports Medicine and Physical Fitness, (2004) 44(1) pp.15-22 RAE2008

A modified TRIMP to quantify the in-season training load of team sport players

Thatcher, Rhys, et al., 'A modified TRIMP to quantify the in-season training load of team sport players', Journal of Sport Sciences, (2007) 25(6) pp.629-634 RAE2008

Rationale and design of the Exercise Intensity Trial (EXCITE): A randomized trial comparing the effects of moderate versus moderate to high-intensity aerobic training in women with operable breast cancer.

BACKGROUND: The Exercise Intensity Trial (EXcITe) is a randomized trial to compare the efficacy of supervised moderate-intensity aerobic training to moderate to high-intensity aerobic training, relative to attention control, on aerobic capacity, physiologic mechanisms, patient-reported outcomes, and biomarkers in women with operable breast cancer following the completion of definitive adjuvant therapy. METHODS/DESIGN: Using a single-center, randomized design, 174 postmenopausal women (58 patients/study arm) with histologically confirmed, operable breast cancer presenting to Duke University Medical Center (DUMC) will be enrolled in this trial following completion of primary therapy (including surgery, radiation therapy, and chemotherapy). After baseline assessments, eligible participants will be randomized to one of two supervised aerobic training interventions (moderate-intensity or moderate/high-intensity aerobic training) or an attention-control group (progressive stretching). The aerobic training interventions will include 150 mins.wk⁻¹ of supervised treadmill walking per week at an intensity of 60%-70% (moderate-intensity) or 60% to 100% (moderate to high-intensity) of the individually determined peak oxygen consumption (VO₂peak) between 20-45 minutes/session for 16 weeks. The progressive stretching program will be consistent with the exercise interventions in terms of program length (16 weeks), social interaction (participants will receive one-on-one instruction), and duration (20-45 mins/session). The primary study endpoint is VO₂peak, as measured by an incremental cardiopulmonary exercise test. Secondary endpoints include physiologic determinants that govern VO₂peak, patient-reported outcomes, and biomarkers associated with breast cancer recurrence/mortality. All endpoints will be assessed at baseline and after the intervention (16 weeks). DISCUSSION: EXCITE is designed to investigate the intensity of aerobic training required to induce optimal improvements in VO₂peak and other pertinent outcomes in women who have completed definitive adjuvant therapy for operable breast cancer. Overall, this trial will inform and refine exercise guidelines to optimize recovery in breast and other cancer survivors following the completion of primary cytotoxic therapy. TRIAL REGISTRATION: NCT01186367.

Neuronal Survival of the Fittest: The Importance of Aerobic Capacity in Exercise-Induced Neurogenesis and Cognition

It is commonly accepted that aerobic exercise increases hippocampal neurogenesis, learning and memory, as well as stress resiliency. However, human populations are widely variable in their inherent aerobic fitness as well as their capacity to show increased aerobic fitness following a period of regimented exercise. It is unclear whether these inherent or acquired components of aerobic fitness play a role in neurocognition. To isolate the potential role of inherent aerobic fitness, we exploited a rat model of high (HCR) and low (LCR) inherent aerobic capacity for running. At a baseline, HCR rats have two- to three-fold higher aerobic capacity than LCR rats. We found that HCR rats also had two- to three- fold more young neurons in the hippocampus than LCR rats as well as rats from the heterogeneous founder population. We then asked whether this enhanced neurogenesis translates to enhanced hippocampal cognition, as is typically seen in exercise-trained animals. Compared to LCR rats, HCR rats performed with high accuracy on tasks designed to test neurogenesis-dependent pattern separation ability by examining investigatory behavior between very similar objects or locations. To investigate whether an aerobic response to exercise is required for exercise-induced changes in neurogenesis and cognition, we utilized a rat model of high (HRT) and low (LRT) aerobic response to treadmill training. At a baseline, HRT and LRT rats have comparable aerobic capacity as measured by a standard treadmill fit test, yet after a standardized training regimen, HRT but not LRT rats robustly increase their aerobic capacity for running. We found that sedentary LRT and HRT rats had equivalent levels of hippocampal neurogenesis, but only HRT rats had an elevation in the number of young neurons in the hippocampus following training, which was positively correlated with accuracy on pattern separation tasks. Taken together, these data suggest that a significant elevation in aerobic capacity is necessary for exercise-induced hippocampal neurogenesis and hippocampal neurogenesis-dependent learning and memory. To investigate the potential for high aerobic capacity to be neuroprotective, doxorubicin chemotherapy was administered to LCR and HCR rats. While doxorubicin induces a progressive decrease in aerobic capacity as well as neurogenesis, HCR rats remain at higher levels on those measures compared to even saline-treated LCR rats. HCR and LCR rats that received exercise training throughout doxorubicin treatment demonstrated positive effects of exercise on aerobic capacity and neurogenesis, regardless of inherent aerobic capacity. Overall, these findings demonstrate that inherent and acquired components of aerobic fitness play a crucial role not only in the cardiorespiratory system but also the fitness of the brain.

The Effects of Cilostazol on Exercise-induced Ischaemia-reperfusion Injury in Patients with Peripheral Arterial Disease

Objectives: Cilostazol improves walking distance in peripheral arterial disease (PAD) patients. The study objectives were to assess the effects of cilostazol on walking distance, followed by the additional assessment of cilostazol on exercise-induced ischaemiaereperfusion injury in such patients.

Methods: PAD patients were prospectively recruited to a double-blinded, placebo-controlled trial. Patients were randomised to receive either cilostazol 100 mg or placebo twice a day. The primary end-point was an improvement in walking distance. Secondary end-points included the assessment of oxygen-derived free-radical generation, antioxidant consumption and other markers of the in?ammatory cascade. Initial and absolute claudication distances (ICDs and ACDs, respectively) were measured on a treadmill. In?ammatory response was assessed before and 30 min post-exercise by measuring lipid hydroperoxide, ascorbate, atocopherol, b-carotene, P-selectin, intracellular and vascular cell-adhesion molecules (I-CAM and V-CAM), thromboxane B2 (TXB2), interleukin-6, interleukin-10, high-sensitive C-reactive protein (hsCRP), albuminecreatinine ratio (ACR) and urinary levels of p75TNF receptor. All tests were performed at baseline and 6 and 24 weeks.

Results: One hundred and six PAD patients (of whom 73 were males) were recruited and successfully randomised from December 2004 to January 2006. Patients who received cilostazol demonstrated a more signi?cant improvement in the mean percentage change from baseline in ACD (77.2% vs. 26.6% at 6 weeks, pZ0.026 and 161.7% vs. 79.0% at 24 weeks, pZ0.048) as compared to the placebo. Cilostazol reduced lipid hydroperoxide levels compared to a placebo-related increase before and after exercise (6 weeks: pre-exercise: 11.8% vs.

Validity and reliability of cardiorespiratory measurements recorded by the LifeShirt during exercise tests

The LifeShirt is a novel ambulatory monitoring system that records cardio respiratory measurements outside the laboratory. Validity and reliability of cardiorespiratory measurements recorded by the LifeShirt were assessed and two methods of calibrating the LifeShirt were compared. Participants performed an incremental treadmill test and a constant work rate test (65% peak oxygen uptake) on four occasions (>48 In apart) and wore the LifeShirt, COSMED system and Polar Sport Tester simultaneously. The LifeShirt was calibrated using two methods: comparison to a spirometer; and 800 ml fixed-volume bag. Ventilation, respiratory rate, expiratory time and heart rate recorded by the LifeShirt were compared to measurements recorded by laboratory equipment. Sixteen adults participated (6M: 10F); mean (SD) age 23.1 (2.9) years. Agreement between the LifeShirt and laboratory equipment was acceptable. Agreement for ventilation was improved by calibrating the LifeShirt using a spirometer. Reliability was similar for the LifeShirt and the laboratory equipment. This study suggests that the LifeShirt provides a valid and reliable method of ambulatory monitoring. (C) 2009 Elsevier B.V. All rights reserved.

An orientation free adaptive step detection algorithm using a smart phone in physical activity monitoring

In this paper we present an Orientation Free Adaptive Step Detection (OFASD) algorithm for deployment in a smart phone for the purposes of physical activity monitoring. The OFASD algorithm detects individual steps and measures a user’s step counts using the smart phone’s in-built accelerometer. The algorithm considers both the variance of an individual’s walking pattern and the orientation of the smart phone. Experimental validation of the algorithm involved the collection of data from 10 participants using five phones (worn at five different body positions) whilst walking on a treadmill at a controlled speed for periods of 5 min. Results indicated that, for steps detected by the OFASD algorithm, there were no significant differences between where the phones were placed on the body (p > 0.05). The mean step detection accuracies ranged from 93.4 % to 96.4 %. Compared to measurements acquired using existing dedicated commercial devices, the results demonstrated that using a smart phone for monitoring physical activity is promising, as it adds value to an accepted everyday accessory, whilst imposing minimum interaction from the user. The algorithm can be used as the underlying component within an application deployed within a smart phone designed to promote self-management of chronic disease where activity measurement is a significant factor, as it provides a practical solution, with minimal requirements for user intervention and less constraints than current solutions.

Impact of exercise training on cancer-induced cardiac dysfunction

Cachexia is a complex syndrome characterized by severe weight loss frequently observed in cancer patients and associated with poor prognosis. Cancer cachexia is also related to modifications in cardiac muscle structure and metabolism leading to cardiac dysfunction. In order to better understand the cardiac remodeling induced by bladder cancer and the impact of exercise training after diagnosis on its regulation, we used an animal model of bladder cancer induced by exposition to N-butyl-N-(4-hydroxybutyl)-nitrosamine (BBN) in the drinking water. Healthy animals and previously BBN exposed animals were submitted to a training program in a treadmill at a speed of 20m/min, 60 min/day, 5 days/week during 13 weeks. At the end of the protocol, animals exposed to BBN presented a significant decrease of body weight, in comparison with control groups, supporting the presence of cancer cachexia. Morphological analysis of the cardiac muscle sections revealed the presence of fibrosis and a significant decrease of cardiomyocyte’s cross-sectional area, suggesting the occurrence of cardiac dysfunction associated with bladder cancer. These modifications were accompanied by heart metabolic remodeling characterized by a decreased fatty acid oxidation given by diminished levels of ETFDH and of complex II subunit  from the respiratory chain. Exercise training promoted an increment of connexin 43, a protein involved in cardioprotection, and of c-kit, a protein present in cardiac stem cells. These results suggest an improved heart regenerative capacity induced by exercise training. In conclusion, endurance training seems an attractive non-pharmacological therapeutic option for the management of cardiac dysfunction in cancer cachexia.

Validity and Test –retest Reliability of the TIVRE-Basket® Test for the Determination of Aerobic Power in Elite Male Basketball Players

The aims of this study were to 1) determine the relationship between performance on the court-based TIVRE-Basket® test and peak aerobic power determined from a criterion lab-based incremental treadmill test and 2) to examine the test-retest reliability of the TIVRE-Basket® test in elite male basketball players. To address aim 1, 36 elite male basketball players (age 25.2 + 4.7 years, weight 94.1 + 11.4 kg, height 195.83 + 9.6 cm) completed a graded treadmill exercise test and the TIVRE-Basket® within 72 hours. Mean distance recorded during the TIVRE-Basket® test was 4001.8 + 176.4m, and mean VO2 peak was 54.7 + 2.8 ml.kg.min-1, and the correlation between the two parameters was r=0.824 (P= <0.001). Linear regression analysis identified TIVRE-Basket® distance (m) as the only unique predictor of VO2 peak in a single variable plus constant model: VO2 peak = 2.595 + ((0.13* TIVRE-Basket® distance (m)). Performance on the TIVRE-Basket® test accounted for 67.8% of the variance in VO2 peak (t=8.466, P=<.001, 95% CI 0.01 - 0.016, SEE 1.61). To address aim 2, 20 male basketball players (age 26.7±4.2; height 1.94±0.92; weight 94.0±9.1) performed the TIVRE-Basket® test on two occasions. There was no significant difference in total distance covered between Trial 1 (4138.8 + 677.3m) and Trial 2 (4188.0 + 648.8m; t = 0.5798, P = 0.5688). Mean difference between trials was 49.2 + 399.5m, with an ICC of 0.85 suggesting a moderate level of reliability. Standardised TEM was 0.88%, representing a moderate degree of trial to trial error, and the CV was 6.3%. The TIVRE-Basket® test therefore represents a valid and moderately reliable court-based sport-specific test of aerobic power for use with individuals and teams of elite level male basketball players. Future research is required to ascertain its validity and reliability in other basketball populations e.g. across age groups, at different levels of competition, in females and in different forms of the game e.g. wheelchair basketball.

Symmetry and order parameter dynamics of the human odometer

Bipedal gaits have been classified on the basis of the group symmetry of the minimal network of identical differential equations (alias cells) required to model them. Primary bipedal gaits (e.g., walk, run) are characterized by dihedral symmetry, whereas secondary bipedal gaits (e.g., gallop-walk, gallop- run) are characterized by a lower, cyclic symmetry. This fact has been used in tests of human odometry (e.g., Turvey et al. in P Roy Soc Lond B Biol 276:4309–4314, 2009, J Exp Psychol Hum Percept Perform 38:1014–1025, 2012). Results suggest that when distance is measured and reported by gaits from the same symmetry class, primary and secondary gaits are comparable. Switching symmetry classes at report compresses (primary to secondary) or inflates (secondary to primary) measured distance, with the compression and inflation equal in magnitude. The present research (a) extends these findings from overground locomotion to treadmill locomotion and (b) assesses a dynamics of sequentially coupled measure and report phases, with relative velocity as an order parameter, or equilibrium state, and difference in symmetry class as an imperfection parameter, or detuning, of those dynamics. The results suggest that the symmetries and dynamics of distance measurement by the human odometer are the same whether the odometer is in motion relative to a stationary ground or stationary relative to a moving ground.

Measurement of 13CO2 in expired air as an index of compliance to a high carbohydrate diet naturally enriched in 13C.

The aim of this study was to determine whether breath 13CO2 measurements could be used to assess the compliance to a diet containing carbohydrates naturally enriched in 13C. The study was divided into two periods: Period 1 (baseline of 4 days) with low 13C/12C ratio carbohydrates. Period 2 (5 days) isocaloric diet with a high 13C/12C ratio (corn, cane sugar, pineapple, millet) carbohydrates. Measurements were made of respiratory gas exchange by indirect calorimetry, urinary nitrogen excretion and breath 13CO2 every morning in post-absorptive conditions, both in resting state and during a 45-min low intensity exercise (walking on a treadmill). The subjects were 10 healthy lean women (BMI 20.4 +/- 1.7 kg/m2, % body fat 24.4 +/- 1.3%), the 13C enrichment of oxidized carbohydrate and breath 13CO2 were compared to the enrichment of exogenous dietary carbohydrates. At rest the enrichment of oxidized carbohydrate increased significantly after one day of 13C carbohydrate enriched diet and reached a steady value (103 +/- 16%) similar to the enrichment of exogenous carbohydrates. During exercise, the 13C enrichment of oxidized carbohydrate remained significantly lower (68 +/- 17%) than that of dietary carbohydrates. The compliance to a diet with a high content of carbohydrates naturally enriched in 13C may be assessed from the measurement of breath 13CO2 enrichment combined with respiratory gas exchange in resting, postabsorptive conditions.